*examines his season passes for both and decides he's probalby qualified to jump in on this one*
Most importantly, Lake Compounce has Boulder Dash, and if you haven't been on that yet...
SFNE has some good coasters, but they're nothing really out of the ordinary. Even Superman is one of several clones, albeit damn good clones. Boulder Dash is the only coaster of it's kind, though. Until you've done close to 60 mph with trees and the rocky mountainside flying by what seems like inches from your face, you don't know how good a wooden coaster can be.
SFNE is the larger park by far, but I've never been that thrilled with it. I used to love it when it was Riverside Park. When Six Flags took over, they added a lot of amazing rides, but something about the park just kinda died, IMO. I guess I just don't really like the Six Flags atmosphere as much.
Objectively, you could argue for either. In favor of SFNE, they have Superman. They have the Cyclone, although that's not the ride is used to be before Six Flags got to it. The Nightwing, their Huss Flyaway, is worth riding. They also have quite a large water park there, with a new Water Coaster this year that's supposed to be good, but I haven't had a chance to get on it yet. As far as the staff and atmosphere...meh. Supposedly they're working on improving it, but I've never been impressed at all. Food and such is overpriced, but not horribly.
In favor of Lake Compounce...well, there's Boulder Dash, like I already mentioned. They also have the Wildcat, a nice little classic PTC coaster that they've kept up fairly well. Ghost Hunt is a bit on the lame side, but all the more fun for it. There's also the scenery; the park fits right in between Compounce Mountain and the lake. They have a decent water park there as well, and it's also one of the last amusement parks I know of that still have a beach where you can go swimming in the lake. The Lake gets all the points for atmosphere, the staff there has always been very cheerful and friendly with the guests. The food there is very inexpensive for a park, and quite good for the most part.
Basically, if you're looking for extreme rides, it's no contest; you definitely want SFNE. If you're looking for a smaller, "nicer" park, or the best woodie on the east coast (or anywhere, IMHO), go with the Lake. I personally prefer The Lake, but that's just my own opinion.