You guys really don't understand Long Island. Looking at a map isn't going to help you. No, it's not like living in Pennsylvania.
The area around Stony Brook is served by two train lines (LIRR) - the Port Jefferson branch and the Ronkonkoma branch. The Port Jeff train stops right on the campus of Stony Brook, basically, but it takes about 1 hour 50 minutes to get to Penn Station. The Ronkonkoma branch is about 15-20 minutes from Stony Brook by car, and there are trains running every hour off-peak and more frequently during peak hours. The trip takes about 60-75 minutes (peak-off peak). What people don't understand is that getting to midtown Manhattan in an hour is actually a great thing. There are plenty of places within NYC that are farther away, by subway, than that. You could live somewhere in Brooklyn or Queens, and spend 60 minutes or more on the subway getting where you need to go. Hell, you could live in Manhattan and spend 50 minutes on the subway or bus getting where you need to be in Manhattan. Thousand of people commute each day from Long Island to the city. It's no big deal. In fact, it's preferable. People move to Long Island for a reason. If you want to drive, it might take you 45 minutes with no traffic, but two or more hours at rush hour.
Now, it is the suburbs, but I'm not sure exactly what people imagine when they say that. Within five minutes of Stony Brook you have everything you need to function comfortably. Five minutes. You've got a mall with your standard set of stores. You've got a Barnes and Noble, Borders, Whole Foods, Trader Joe's, several other supermarkets, several movie theaters, and a bunch of other stores that you might need. Miles of beach are about 20 minutes away. There are research opportunities at Stony Brook, and then there is Brookhaven National Lab and Cold Spring Harbor.
Living on Long Island can be expensive. There are a lot of areas around that are fairly affluent. Apartments can be expensive. Going to the city is expensive - train tickets will run you $24-28 round trip. You need a car. But the areas around Stony Brook (from the LIE up, so within about 10-15 miles of the school, to make it convenient) are very safe and nice.
Stony Brook serves a large population. You will see all kinds of patients. If you yearn to see gang members, you'll get to see them.
If you want to go clubbing every night, then living on Long Island is going to be a bummer. But if you just want to go to the city to hang out a few times a week, or on the weekends, then you're really no worse off than people living in the five boroughs. There are always trade-offs here between money, safety and proximity/time.
And, if you have a load of cash, you could just live in Manhattan and commute to Stony Brook.