We stayed in the Aolcantara marina and found it not to be a problem. Not too far to walk to public transport, shops etc and we used it as a base for about a week without a problem. Most of the marinas there suffer from noise from the bridge which has a metal grating deck and produces a loud noise like a swarm of bees. This is worse during rush hour but not too bad at night as there is less traffic on the bridge.
Still recommend it though, the swing bridge wasn't a problem as times of opening are advertised and easy to work to. From memory there is a waiting pontoon either side of the bridge. Good luck and enjoy Lisbon, a stunning city!
Growing old - disgracefully!