I have done the ride from sandy hook to cape may ferry several times, and also from Baltimore to Lewes, DE, the other end of the ferry.
For the NJ side, you have lot of options but the coastal route is nice. Stick right be the coast through seaside heights; then cut over to toms river, take route 9 through Tuckerton. You then must cut inland to lower bank, where you can cross the river. Then you have a choice; inland route straight down, or take the route 30 bridge to Atlantic city and go down the coast to wildwood before cutting across to the ferry.
A great resource is njbikemap.com. The guy has rated virtually very road in NJ.
Once in DE, you have two choices: head pretty much due west on back roads, then take a car service across the bay bridge (they'll shuttle you over for around $15, the number used to be on the MD state transportation page but if you search for taxi bay bridge you should find it.). From there there is a great bike path heading northwest to BWI, and google maps gets you into Baltimore using a pretty good route from there.
The alternative is to head northwest from Lewes, through Chesapeake city, md, over the canal and then north to Elkton, west on 40 to perryville rd, then west again past port deposit to the conowingo dam, which lets you cross the Susquehanna on a bike. Route 1 south will get you to baltimore fine, or you can take some backroads as you get closer to the city. From the north, falls road gets you downtown pretty good.
Ive got most of these routes mapped out but I'm on my iPad right now; let me know what you'd like and I can get them to you (can one post PDFs tmthese fora?)