Given your 2 year timeframe, I would suggest you look at 2-4 locations and move between them. Each area of the Chesapeake has it's own unique charms, attractions, and downsides.
My preference would be to move the boat occasionally to a new locale and then explore what that area has to offer. Frankly, whether the airport is 45 or 90 min away won't matter nearly as much as whether the anchorage you want to explore is within easy sailing range for a day or weekend trip.
As you can tell from the other responses, there are lots of fantastic places both to explore and to keep a boat. We've been in the Annapolis
area and have kept boats on the South, Severn and Magothy rivers and are now on Whitehall Creek. But our favorite spots are still on the Eastern Shore: Oxford, St Michaels, Cambridge, etc.
Of course, we also envy those folks living either north or south of us on the Bay! The water's always blue-er... or something like that.