There is no actual T stop in the North End itself, but Aquarium on the Blue Line and Haymarket on the Orange and Green Lines are indeed the closest. It's only a block or two to the North End from either. The North End is quite safe, as is most of the Downtown area. Just use your street smarts as you would in any citry.
Sure... Both are in the city, so...keep your wits about you, etc. etc. I'd prefer Haymarket over the Aquarium late at night only becuase it's more heavily traveled at that hour. True, you mght run into a few unsavory characters at Haymarket, but I'd rather do so in a crowd than traverse a lonely station. Haymarket is a starting point for loads of buses that go up to Lynn, etc. so there's always people around. There are a few bars and restaurants near the waterfront by the Aquarium but... not many. It's not as well traveled.
One big negative of the Charlie Card system is that it's harder to find T employees . Before you knew there'd be a token guy in the booth. Now, you walk down there and see mostly card kiosks. Sometimes there are employees in view (and T cops) but not always.
Don't forget about the North Station T stop--both Green and Orange Lines. Go to mbta.com for all maps, fare info, etc. Also, to echo other post-ers remarks about safety--the potential for trouble should always be in the back of your mind, but those areas are fine at night.
Although both Haymarket and Aquarium are convenient to the North End, Haymarket (Green Line) will have more frequent service, especially at night. Which station you use really depends upon where you are coming from. If you are on a particular subway line, it is not worth changing trains to get to a station on the other line. (If you are on the Red Line, switch to Green inbound at Park St.)
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