For what it's worth, I'm Jewish too, also a fan of unique Biblical names, and Noah is still on my short list after all its use. The thing is, it's been in the top 100 since 1995 and has been rising since then. There's no getting around the fact that it's a pretty common name, as names go, and past trends indicate that it wouldn't have just fallen off the top 10 list this year. The flip side is that since so many parents are hunting for unique names, Noah was still only given to less than 1% of baby boys this year, at the height of its popularity!
You shouldn't feel bad about giving your son the name Noah. It's a wonderful, strong name with a lot of history and a great story behind it. Despite its popularity, it's not another Aidan/Aiden/Ayden/Aydan/Aedyn/Aighdynne/etc. I've only ever met two Noahs in my life, one of whom is Jewish. Besides, among all the sound-alike Aidan/Braden/Jaden/Caden/Haydens, Noah has a unique sound to it that stands out. It's a name that can be taken seriously and ages well. Your son will thank you. :)
Vote on my PNL! http://www.behindthename.com/pnl/69271 "Do not argue with an idiot. He will drag you down to his level and beat you with experience."