Hi Emoreira,
I do a lot of diving as you are describing in uncharted lakes and if you click on the link in my sig line I am also involved in a more in depth project for one specific lake. I can offer a few suggestions.
The Fishfinder/depth sounder is a good idea if you have access to a boat with one. This will help you determine the general profile of the bottom and to detect any large objects or features.
Do some research and see if you can't find a bathymetric map for the lake. This shows the depth contours. It would save you a lot of groundwork.
Break your lake up into sub sections to tackle one at a time instead of trying to map a whole lake at once. Then you can descibe each area in more detail and focus your efforts better.
I generally do two types of exploratory dives. The first is a straight down descent from the shore to determine the slope profile, littoral/benthic zone interface and bottom composition. Once I do this I usually swim around a bit and then ascend at a different spot to see what the slope is like there.
Next I dive down from the same access point to a desired depth and follow that depth contour in one direction till I reach my turn pressure, ascend to a shallower predetermined depth contour and follow that back to my exit point. For example: Descend to 60', swim that contour, turn, ascend to 30', swim that contour back to start, exit. By doing this repeatedly you can soon develop a general understanding of the basic features of the lake and plot them on a map. What you miss are the open water portions but those really need to be covered with the fishfinder/depth sounder first.
Using GPS and marker bouys sounds cool but it isn't really neccisary until you are well on your way to creating a defined overview of the area. It's best to go from known to unknown systematically and not just swim around willy nilly hoping to bump into something to mark. First it's just old fashioned foot (fin) work. The only time you might need to mark something from the surface is if you come across something unique while swimming the contours. I did this a while ago when I found portions of an old Bailey bridge. I knew the depth but not the position in the water. In that particular case I just did a short dive wherein I swam to the object underwater, located it, swam directly upslope to the surface, and found a reference point on land. Problem solved.
Be sure to observe the shoreline first to see if there are any barriers to exiting earlier than intended if you need to.
I don't know about your region but in my area the biggest dangers posed in lakes are hypothermia due to cold (especially under the thermoclines), entanglement in fishing line and entanglement in tree limbs (due to low vis conditions). In the summer, it is being hit on the surface by boaters.
Good luck with your efforts if you choose to go ahead. Let me know if I can help in any way.
Dale.