I'm still fairly new to New York and very new to Brooklyn. Are there any good long-ish routes that don't go through Manhattan?

Sorry if this is not the right channel. The UI of the forums didn't make it clear where the discussion would be posted.

When I lived in Crown Heights and wanted a change, I would head south on Bedford, east on Ave U, south on Flatbush, across the bridge, and then west into Breezy Point (just roll past the guards) and head to the tip.  take a break by the beach where there is NOBODY and enjoy not seeing a human for a few moments.   Head back east towards the Rockaways.  You can continue east and then go north on Cross Bay Blvd, which has a bike lane.  Getting back to your apt. is then choose your own adventure.  You can get a good 40 miler just with this loop.

And its generally windy ... Like Houston

I second Scott's suggestion. I rely on loops around Jamaica Bay for much-needed variety and its my go-to when I want to get in a 2 or 2.5 hour endurance ride with sub-60 minute tempo intervals. Riding the Bay is surprisingly easy to tailor to your needs and desires. 

• the basic (counter-clockwise) loop
• clockwise loop - you should have the cycling path next to the Belt Pkwy pretty much to yourself; no traffic lights for miles
• extra laps up and down the peninsula for longer tempo intervals - repeatable ad infinitum all the way out to Breezy Point like Scott said; good practice feeling out head-, tail- and crosswinds

Basically any time not between Memorial Day and Labor Day it's very lightly trafficked, but even in high summer it's hard not to enjoy a ride along the beach if you're content to defer to cruisers and daytrippers. Whenever you go, you'll have great views of the Manhattan skyline and the water around you. And when you take your cyclocross bike, great little spots to ride off-road. Sand, obviously, but also crushed gravel paths at Tilden, grass double-track in the north woods at Floyd Bennett Field, and weird lumpy service roads through Spring Creek Park in Howard Beach.