Eastern end of Brooklyn Bridge is indeed a good place for cityscapes. There's a viewing platform/pier south of the bridge on Brooklyn side where there's plenty of room for tripod. You can see the exact location on the main page of my site in my signature by zooming into Manhattan on the map. I've also seen good shots taken from Empire Fulton Ferry State Park just north of Brooklyn Bridge.
Alternatively you can go to Hoboken or Union City in Jersey (west of Manhattan) by ferry. There's a stunning panoramic view from Hamilton Park from a hillside down to Manhattan - don't have the picture up on my site, yet. Also plenty of room for tripod, and a lesser-frequented site than Brooklyn Bridge. Take a ferry to Port Imperial/Weehawken, and climb up stairs on the steep hill, take a right on top.
Police presence is actually desirable in many parts around New York for your safety. Hamilton Park (and the viewing platform in Brooklyn Heights) were patrolled by police at and right after sunset when I visited, so you should be safe.
Similarly great views from the harbor itself in Weehawken which has a small waterfront park by the parking lot: you can get within a few meters from the waterline. Not much police presence there, though. I'm not sure if that area has high crime rate; I saw lone female joggers well after dark so I assume no.
Many more opportunities in the city, it's one of the most picturesque cities there is. I think it's better to avoid setting up a tripod on busy sidewalks as I'm sure you'll get hassled over that - not only by police 
If you only have 1.5 days, I'd recommend doing online scouting on Flickr or Panoramio to see what other places you'd like to capture.
Manhattan Nighttime Skyline from Brooklyn Heights (zoomable alternate view under Panoramas).
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I appreciate the suggestions. I wasn't able to make the trip last month as planned. But plan on heading to NYC this Friday as I have to make another trip to Toronto for work. My timeline will be the same - have about 1 1/2 days in NYC.
Nice shots and also liked the shots on your website. Is the Eastern Side of Brooklyn Bridge where you took the "Brooklyn Bridge !" shot? Love the warm light - Is that taken early morning or sunset? Are the light for the twin beams always on, or was that only for the memorial?
Given the amount of time I have, and where I was staying I was thinking of trying to do the following:
-going to either the Empire State Building or Top of the rock for sunset (will probably only have one sunset), brooklynn bridge for one of the sunrises - haven't decided on the other
-take evening shots from your Brooklyn heights suggestions or from NJ on the two nights I'll have there.
- Also would like to hit Times square at night as well.
Any other suggestions for can't miss locations? Did you take the subway to commute, or drive? Is parking still a problem at night or sunrise times?
Equipment wise what would you suggest I take? I don't want to take my big Gura Gear backpack, which holds my 1DIV, 5DII/grip, 24L TSE, 24L, 85L, 70-200 2.8LIS, 24-105L and teleconverter + plus my RR pano kit.
I was thinking of taking a smaller bag (Tamrac Evolution
which that will allow me to take a 5DII/16-35L and a 1DIV with either a 70-200 f2.8LIS or a 24-105L mounted and the other lens unattached, a couple of polarizers plus one flash. Do you think that this would be a good setup to take, or will I miss the 24TSE (i.e. for stitching Panos) or the 85L (street shots)? I would like to shoot some panoramics, but am not sure if it makes sense to carry around my RR pano kit, or if most of the Pano oppertunities are well suited to using the 24TSE focal length. I could always bring the other lenses along and carry them in my computer bag, but would like to keep things to a mimimal, as I'm expecting to have to do a lot of walking or commute on the subway.
