Wow. I'm late to this local request.
I would recommend the 17 Hundred 90 Inn if you would like to try something completely different. Just bring your plasma ray guns for the ghosts! I had dinner in their restaurant and throughly enjoyed the ambiance. [A freaky side note: A colleague wanted to try two of the desserts. The server brought a little sample of one but decorated it as a birthday special to "get it out of the kitchen free". Unbeknownst to anyone in our party or at the restaurant, it really was her birthday!] It's a little further walk to the main areas, but it keeps it a bit quieter. It's about 3 blocks to the East end of River Street. Though on Tripadvisor as a B&B, they only offer continental self serve fare for breakfast. It's a bit on the costlier side, but it's an experience not to miss. They are about a 3 minute walk to the Connect on the Dot free shuttle service that runs around the downtown area (Note: it runs a circuituous route in one direction only).
For about 70% more and located across the street from 17 Hundred 90 is the extremely elegant, historical Kehoe House which is fantastic. They DO include a full breakfast.
There are several others in the area that are unique to Savannah like the River Street Inn and would probably compete well with the bigger chains. Most of the unique, elegant locations will be in the $180-$300 range. I really think that the 1790 is the best value in the area. Arguably the nicest is the new Bohemian but it will set you back around $430 for a river view room.
As for the taxis, I have not ever heard of any complaints. Unfortunately, with most arrivals being between 7 PM and 7 AM, the city hasn't set up any sort of bus or transit system to connect the station to the rest of the city. Like many places, this station is in a very industrial area. The history of the station is interesting. There was a Union Terminal in downtown Savannah until the early 60s when they decided to demolish it for the I-16 ramp into town. So the city paid Atlantic and Seaboard to move the passenger service to its current location. It's a pretty nice station and well kept, but being 60's architecture, it seems to bring out the utilitarian style of the time. The mosaic on the ouside and the murals on the inside of the station are quite facinating, though, as are the disfunctional but preserved wooden phone booths.
The Greyhound Bus Station is quite on the opposite side of town, on the West side near the sprawl of Savannah College of Art and Design. Here you will find perhaps cheaper yet perhaps a bit more uncomfortable accomodations. Thunderbird Inn is across the street, but I don't think I'll recommend it. It seems to be out of place in Savannah, more fitting for a Route 66 motel somewhere in Arizona... The reviews are mixed, YMMV. You'll be about 5 minutes walking from the Visitor Center which has a Connect the Dot stop. It's also close to the Civic Center and the railroad museum as well as a few nice restaurants. You're not really walking distance to the River and it is a much busier part of town. The Best Western Plush Savannah Historic District is not too far, but it's pretty basic as motels go and probably over priced for its location.
Finally, I have no problems at all with the Inn at Ellis Square. It is right near the River, near City Market, about a mile from Greyhound, and not too far from the Connect the Dot.
Hope all this helps!
