Here is my take... It takes time and patience to get a good deal from someone who can be trusted. I'd get as many quotes as possible before deciding. Several of the things to watch out for:
1- Fully insured transporter for at least the full value of the boat, and with liability insurance. Get a copy of the certificate in advance.
2- Don't agree to pay fully in advance. First one I did was 100% COD, not a penny upfront, while on the second one I put down like 20%. I wouldn't pay more than that in advance, you want to make sure that your boat gets there in good shape. They may say that's not their policy, but both times when pushed they agreed to those terms.
3- I like having the contact info of the driver, in both instances I was able to talk to him by cell phone and check on his progress.
Both of my moves (one was a 31' Doral and the other a 29' Tiara) went well. First one was on a flatbed, boat riding backwards, with cockpit cover on, from FL to MN. Only problem was diesel soot and road dirt on the boat, and riding backwards behind the truck made it worse, stuff got under the cover and made the cockpit very dirty, but nothing that a good cleaning didn't take care of. Second time around it was transported on a boat trailer behind a pick-up, riding bow-forward. Again I chose NOT to wrap and the Tiara didn't have a cockpit cover so it just ran cockpit exposed to the elements, from FL to MN. It worked out great. It got here in great shape and I'd almost say "clean", not sure why, maybe the fact that it got rained on on the last couple of days of transport? I think riding bow forward also helped a lot. Given my experience, I would ship with NO WRAP at all just like I did with the Tiara. Shrink wrap can possibly damage the boat if any becomes loose, and the cockpit cover seemed to mostly help to trap dirt when I had the Doral moved.
The company I used the first time is a large dispatcher who moved my Doral, I contacted them directly and chose to go with them based on price. Again, it went well although they showed up a few hours early for pick up and made me scramble. Second one was a smaller operation, and I hired them through uShip (it's a good place to list your transport to get competitive prices). If I recall my first move cost $3,500 while the second one cost $4,250, both from FL to MN and both boats about the same size... One in 2006 and one in 2008 (gas price REALLY HIGH in '08 was the main difference). Northern based transporters seem to be more expensive based on my experience in getting quotes, so it may be worth contacting some people from other regions who may by luck have a boat already going in one direction... Sometimes you can get a deal if it's on a "return" trip. Hope this helps!