Definitely check out Everglades Rentals & Eco Adventures - they are top notch in service and hospitality! Looks like you can stay at their lodge too, appears to be very accomodating. I really enjoyed seeing a few gators - not for the light-hearted!
Quick Tips:
Though I didn't stay at their motel, I did notice several overnighters that seemed very content. It's necessary to be someone who enjoys adventure and has a flair for nature - this isn't for homey-people. I learned a lot from the guides there - don't be afraid to ask! And bring your camera!
Best Way To Get Around:
The canoes seemed to work well in the small waterways ;)
Other than that, the roads looked like they support most vehicles, though I wouldn't take anything too weighty around. My Hyundai rental stayed above ground the entire time.