The aquarium at Riverhead is not tremendous, but it is quite nice and worth a trip. The reef tank there is amazing! Correct me if I am wrong, but the Atlantis Aquarium also operates "Reef Gen" which is a grower and supplier of some very nice corals (available only through retailers, not directly.)
As a former east end Long Islander, and one time Manhattan dweller as well, I can assure you that there is a world beyond New York City. As far as things to do, in the summer the island beats the city hands down! Beautiful beaches, sailing, biking, hiking, botanic gardens, beautiful fall foliage, etc, etc. In fact, I could easily visit eastern Long Island, and not even consider schlepping in to the city to experience the hot, muggy, sweaty weather during July and August.
And don't forget the "Big Duck!"
I grew up on LI (west end/north shore) and it was nice but pretty dull. Coolest place around was a bowling alley called My Fathers Place and the Nassau Coliseum and now their wrecking that!! If I lived in NY, I'd definitely check the place out, but I live in DC and after a 4 hour drive and only a weekend or three days up there, forget it.
Bruce