Dalton- yes I highly recommend Reggie tours. They also have Mayan ruin tours and I think they have zip line tours now. But Reggie's gave us much more for our money than the cruise line tour would have. There are a couple of different entry points into the cave system and Reggie took us to one much further up river than where the ship tour puts in at.
I don't know if you read my review of them, or if it is even available anymore if you do a search, but Reggie won me over. For some reason our booking date got messed up and they did not know we were scheduled for our day. We had Reggie's phone number and we called him.. after figuring out the scheduling mistake, Reggie arranged for another tour guide to bring our party to a meeting point where he was able to pick us up and give us our tour. He had to pay that tour guide for doing so, but did not change what he charged us to do so. If he had not done that we would not have been able to do the tour. That's customer service.
And I understand that some people seem uneasy in Belize City. It is a poor country and the city outside the port terminal area is a bit rough looking, but we have never had a problem there, nor have we heard of people having problems there. I'm not saying you don't need to be careful, but I would not be afraid to venture beyond the port terminal shopping area. However, there really isn't much to see unless you are going on a tour inland.
Yes, you get back in plenty of time. He has multiple van's. Even if your's were to break down at the tubing site, there would be enough time for him to get another out there and then get you back to the cruise terminal.