Thanks for the replies guys, sorry for my lack of response (busy semester!)
I would like the greatest accuracy possibly for the roughly $1000 budget to be used for the GPS and sonar units and equipment (anything needing to get those set up and working). Lowrance seems to have the equipment that would work for this project, and I've seen other research using Lowrance gear.
What I would really appreciate help on, and what will help narrow my options, is learning how Lowrance units with SD cards export data onto a computer, and how I can use those files to create a spreadsheet with depth, lat, and long. I am still a little overwhelmed by all the different file extension names and software for extracting data etc etc.
I will also require a unit that can collect the coordinate and depth data automatically as we drive the boat. Some units just let you sore way-points, but require you to press a button to log them. I am hoping for a unit that can log depth and coordinates once every 1-5 seconds for example.
Thank you for your replies, I hope I haven't responded too late to get more assistance!