We are in Waterford Harbor and recently also looked at marinas in the Galveston area for the same reason, the long slog up and down the ship channel. Harborwalk is really nice and we also considered Galveston Yacht Basin although it seems to have a poor reputation. There is also a marina in Offatts Bayou, Pelican Rest, but very expensive and doesn't allow working on the boat.
We live in Montgomery and seriously considered Harborwalk but decided to stay in Waterford. Two reasons, I absolutely hate I45 and the distance to any stores and restaurants. If you have a new to you boat I think you will appreciate being close to WM, Kemah Hardware, Home Depot and such. Not to mention the choice of restaurants in the area. If I were in your shoes, I would consider a marina on the south side of the lake until you have the boat sorted and then maybe consider one in the Galveston area.