I think the part of Weehawken affected the most by Sandy is the small neighborhood near the exxon station (near the exit to the Lincoln tunnel). The waterfront also flooded but most buildings escaped major damage.

Lincoln Harbor is nice because you're a short walk into Hoboken, there's a whole foods right there, and easy bus/ferry access to nyc (or light rail into Hoboken/JC). A lot of newer buildings, plus more going up as we speak. Downside is rents are high (over $3k for a 1 bedroom).

Port imperial is another solid option - a lot of what I said for Lincoln Harbor also applies here. But it's a bit farther from Hoboken so not really walkable. Same newer buildings, same high rents.

Weehawken above the cliff is much more similar to jersey city heights. Older colonial housing. Limited parking. But gorgeous views by Blvd East. Bus or jitney is the main transportation method to nyc. Rents will be lower unless you're right on Blvd East.