Hands are a no-brainer, most reptilians have something that can easily work like hands if an intelligence was behind their use. As for walking upright, while there are no alligators that can walk upright as far as I'm aware, they are capable of launching themselves straight up out of the water. This tells me they have at least a minimal ability to keep their spine straight in an upright position and could be improved upon if they were to go into a bipedal direction. By the way, in order for them to be pushed into this direction they're likely going to need pressures for longer arms and legs, so I'll leave it to you to determine exactly what made them require it(tree-climbing perhaps?). Their size category is already human-like if not larger so there's nothing to change there, and many species are greenish or brown so there's another thing you won't need to change about alligators.
Living in villages might come naturally to them since they tend to be grouped up anyway, at least when mating season comes. You won't have them do agriculture as most village-type communities do, but you can have them be fishing villages, which will tie in naturally with their swimming capabilities and even if they don't want to swim their ability and natural tendency to remain still and bake in the sun for long periods of time will aid in the proliferation of the use of fishing rods. Once they gain a greater understanding of fish in general they can perhaps build for themselves fish farms, which would aid in the formation of larger and more well fed villages. Feeding the fish would either be done naturally by having the farm be part of a river or from the produce that they'd have in abundance(since they won't eat any of it and won't need as much space for them) from farming plants. Them remaining full carnivores is more plausible as well since things would have had to be pretty dire for such a killing machine to gain traits to tolerate other kinds of foods.
As for communication, alligators can bellow. Now this is generally only for mating purposes as far as I'm aware, but it might be adapted for long range communication between two underwater individuals. The young ones can also do that cute squeak thing, whatever it's called, telling me they at least have the capability for the production of variable sounds. Intelligence + community living would drive them to develop more sophisticated forms of communication anyway, probably some form of speech via variable tone and length bellows if nothing else, so you don't need to think about this too much.
Just about the only thing you may have to handwave is the development of their higher intelligence. Alligators and crocs have been the way that they are for a long time and only severely drastic pressures will move them away from it, pressures severe enough that you're going to need to explain how it affected other creatures if it does ever come up in-setting.