Personally, if I'm staying downtown, I'd just as soon dive with an op that leaves from a downtown pier. If the op will get you to the marina, that may be doable for you too. Deep Blue leaves from a downtown pier, Tres Pelicanos and Blue Magic will get you to the marina. I think their prices are in about the same ballpark. Aldora and Blue XT~Sea leave from a downtown pier, but I think they're both a little more expensive than the other three I mentioned. The differences in price can be accounted for, so there may be considerations, for instance Aldora uses big tanks, so this might make a difference for you. For me, I'd be thinking about convenience issues to make my final decision and would be willing to pay a little more if it was more convenient due to departure times, tank sizes, proximity of my hotel to the dive op or departure point, etc. For instance, and this is just for my tastes, Deep Blue or Blue XT~Sea would work because they leave a little later than the others, from a downtown pier. Deep Blue leaves at 9am and Blue XT~Seas leaves at 8am. Tres Pelicanos will get you to the marina without charge, but you have to be at their shop around 7:40am. For me, that's a little too tight time wise.
My guess is that there are other ops that fit the "leave from downtown or will get you to the marina from downtown" bill, I just don't know who they are off hand.