Well first lets consider what we have to work with, and what we are going to be working against
Dr. Max Patel: One of the human scientists that stayed behind, he provided technical support and advice on the avatar hardware systems. This is the guy likely keeping the base operational and liviable for the remaining humans, and is probably the most vital guy for any future hope of the Na'vi, as he is the guy with the knowledge of the equipment they'll be needing.
Jake Sully: Obviously important as he has gained a huge amount of influence with the Na'vi and has the most knowledge of human military tactics.
Norm Spellman: One of the remaining humans, and probably the least important. The guy is certainly determined to be helpful and perhaps has more guts than brains, but seeing as his avatar got killed and his field of expertice is anthropology, he's really nothing more than a set of hands in this situation.
Possibly the other avatar drivers: At least one avatar is shown at the end of the movie holding a gun while watching the humans being loaded into the remaining shuttle, so we have at least one no name extra set of hands. The avatar camp showed somewhere around a dozen avatars, so there is the possiblity of having them left behind as extra help.
Quatum radio: Two top uses of this device will be in "humanizing" the Na'vi as Tyyr suggested, and in having whatever allies they have on earth sending over any and all details they can get their hands on as to the plans of the RDA. Also any weapons or hardware blueprints for the stereolithography plant would be useful. The humanizing efforts might be well given over to Norm, as after Jake he's probably the human the na'vi are most likely to trust, as he did take part in the actual fighting to save their world.
Hells gate: The mining base, the following stats ripped from the avatar wiki: A pentagonal perimeter fence (each side 2.3382 km or 11.69 km--7.264 miles--total) encloses 9.406 sq km (approx. 3.6317 sq miles). Major weapon towers at each apex provide heavy munitions defense against surface and air intrusions by large hostile Pandoran wildlife, while four smaller towers spaced 250 meters apart along each side handle intrusions by smaller life forms, including burrowing attacks. A cleared, thirty-meter-wide strip surrounds the base, which is regularly patrolled by automatic plant-clearing machinery that keeps the jungle at bay through regular administration of acidic mining byproducts. Slightly more than a third of the site is taken up by the shuttle runway, VTOL pads, hangars, equipment storage areas, and garage structures. A similar area is occupied by the armor bay, vehicle storage sheds, and a light industrial plant mainly used for fabricating parts for mining equipment and ammunition for base defense. The unobtainium refinery complex takes up the western side of the facility. The remainder of Hell's Gate is composed of administrative structures, a barracks for Sec-Ops staff, studio-style apartments for technicians and mine workers, and an airtight condominium for senior staff, as well as Sci Mod that is part of the utilitdor-connected Hab Mod, OPS Center structures. Recreational facilities such as the base commissary (popularly known as Hell's Kitchen) are shared, except for an unpressurised section between the research labs and the landing zone mainly used by members of the avatar program for athletic training.
Stereolithography plant: (also from the wiki) Every piece of human machinery used on Pandora must be made at the Stereolithography plant. Stereolithography is a form of 3D printing which allows the humans to construct practically anything they want as long as they have raw materials. The limited ability of the plant to construct advanced computers is one of the reasons why the humans were not able to use up-to-date technology in their vehicles. If machinery is in need of an update, the blueprints must be brought on an ISV so the plant has a template for the construction. Another thing that must be brought on a starship is some of the more advanced materials used to make the objects, most raw materials are however collected on Pandora.
The immediately incoming ships: Over all threat level is likely pretty low really. Each ship carries up to 100 passangers and 25 crew. Even if half that number is security personel, they're not likely to be much of a threat as they are unarmed. Remember that weapons and other hardware are produced on Pandora by the stereolithography plant, only things like nano-processors, certain drugs, and other materials that can not be made or produced on the moon are shipped.
So the only proper threat the next handful of ships have to offer is in using their shuttles as self guided bombs, which is a gamble, as they use the shuttles to refuel the ship for return trip by skimming through Polyphemus's (the planet pandora orbits around) upper atmosphere to obtain hydrogen and deuterium which they convert into anti-matter. Use these as weapons and fail to reclaim the moon, and you're screwed.
The dedicated military ship coming in 7 years: This is the real threat, all 100 passangers will be fighting men, and all 350 tons of cargo will be military hardware. Aside from conventional tactics, said vessel might also be able to field chemical or nuclear weapons, and possibily from orbit depending on just how much power the RDA really has.
1) The RDA will go bankrupt when their next handful of ships return empty handed, thus making a dedicated military mission impossible to fund.
2) Public pressure from the humanizing efforts results in pandora being legally recognized, with the na'vi as the governing body, forcing the RDA to treat their dealings with them as they would any other government. While possible, not too likely. And even if, the distance and cost will make properly policing such virtually impossible.
3) The fighting option.
a) Start arming and training the na'vi with guns. We saw both Norm and Jake's avatars using heavy machine guns like assualt rifles, so the Stereolithography plant has at least one weapon design it can make that the na'vi can use. Any other weapons that the na'vi can use, or which can be adapted for their use, and which the materials and designs are avalible (either on site already or that can be sent over the Q radio) to produce.
Now obviously, to produce anything, some mining is going to have to be done. For this to happen Jake is going to have to convince the na'vi that a bit of damage now is going to prevent a horrific amount of damage down the line. As to how much mining is done is a matter of how many people have been left behind. I have no way to calculate either a high or low end for how much raw materials can be dug up within the time frame outlined by Tyyr on this, there just isn't the info availible for it.
b) See if it's possible to get someone on earth to send over the plans for missiles and a launch system that could threaten the incoming ships, and see if it could be built. I give this one low odds all around, but it wouldn't hurt to try.
2b) Start producing another shuttle. Whether or not this is doable is up for some debate. We do have Max on hand for some technical expertise, though whether he has any technical knowledge in the right fields for this is unknown. I would say it's largely a matter of just how automated the stereolithography plant is, and if they have the proper electronics on hand. Without a shuttle, the na'vi chances are going to be pretty slim, as the shuttle is the only defense they'll have against orbital attacks, either as the means to get a defensive system in place, or to be used as a threat against the incoming ships. Threatening to set the shuttle auto-pilot on a ramming course against any ship that tries to approach the moon would be a fair deterent, especially against the next handful of ships, as I consider the odds they have any anti-ship weapons on board to be very very low.
Total victory: Bankrupting the RDA, or having the material and manpower on hand to put an orbital defensive system in place. Moderate odds for the first, fairly low for the second, and even if accomplished, the possibility exists for the military fitted ship to have the means to defeat it.
Partial victory: Heavily outfitting and training the na'vi with human weapons and equipment. Against the handful of regular ships coming in, this should be a fair solution, especially if they can get some surface to air stuff put in around the base and the holy tree. Trying to fight a physically superior enemy on their home turf who has a vast numbers advantage and who is more or less equally armed is a losing fight all around. As for the military ship, they likely would be bringing in more advanced weapons than what could be produced on pandora, but they will still be at a disadvantage. If the na'vi were armed with human weapons, even if a bit outdated, it would basically turn any ground war into vietnam, only with the "US side" outragiously outnumbered with backup 6 years away. 100 soliders would not hold out long against thousands of na'vi if the technological gap was closed that much.
Compremise: If the resources, technical knowledge, and/or manpower just aren't availible to acomplish either of the above, then it's time to try making some deals, along the lines of what Tyyr suggested in his post.