Most 2 person rafts are barely designed for two people.  We used rafts to float white water for their resiliency, portability and maneuverability, but developed an aluminum frame for seats and strong oarlocks for rowing.  We used six person rafts, and had only 1-2 people plus all of our camping and other supplies per raft for white water.  On a lake, an aluminum flat bottom boat with strong metal oar locks, place for gas or electric motor if desired, added stability and capacity makes more sense as long as you have some access.  However if remote lakes, you may need less weight, so maybe raft or canoe is needed if you have to carry in.  But if you dont intend to use motor, have a canoe with paddles or raft with strong oarlocks suitable for a row boat.  

A six person raft with oar locks was stable enough to stand up in to see upcoming rapids.  A 2 person raft is narrower and shorter, so not quite as stable, but if you are careful and equipment is not too heavy, you should be ok.  I suggest you contact the local US Forest Service or US Geological Survey or State or Federal Fish and Wildlife as they have hydrologists and fish biologists that may give you pointers, and they have a safety book that handles safety rules and protective gear so you can be reasonably safe.  And if they are interested in what you are doing, they may have equipment you can borrow for research or data they might also want.  Also if going to remote places, let someone know your plans.  

It will largely depend on your actual needs. Deploying a CTD or light probe is not a problem from a ligh raft, but if your research includes the use of more heavy equipment (e.g., big water sampling bottles -Van Dorn type-, or gravity coring) you will definitely go for an inflatable but robust boat with flat bottom (i.e., Zodiak or similar). These boats allow you to attach a light electric motor and to keep considerable equipment with two persons. I know, from my own experience, how difficult and risky may be working in a lake with a light raft, especially if working in mountain lakes with adverse weather conditions. I'm not sure about prices in the US, but in Europe you can have a compact boat (Cadet or similar) for less than 1,000 €.

Here's a couple of models that we have in our Institute (both of them used regularly in lake research for years):

http://www.zodiac-nautic.com/en/shop/produits/accessories/cadet/

http://www.zodiac-nautic.com/en/shop/produits/boats/classic-en/classic-mark-i/

 Regards,

Thanks for the answers, folks. I've ordered an Alpacka and will see if that does the trick! For larger deployments, something more rugged may be necessary...

I don't have experience deploying equipment from Alpackas, but I can tell you from professional and personal experience that those rafts are rugged and perform very well for their intended tasks. My wife and I own the traditional whitewater versions and have paddled them in very remote and challenging locations across Alaska. Additionally, our geology program has one that we have used to convey us across flat and whitewater with good results. Prospecting for new fossil locations via raft is a hoot! 

From our shared experience, Dan, don't forget that bears like the looks and smell of rafts, especially new ones that have never even been aired up (I still have that cheap thing). Make sure to carry the patch kit! I'd also recommend that you acquire Tyvek tape. I don't understand why it works so well, but it works very well when it comes to field repairs of bad holes or rips in Alpackas. 

Thanks Denny - I definitely do remember our holey raft! I also bought an electric bear fence for this summer. Hopefully that'll keep them at bay!