To the OP: short answer - I'd buy a bottle at a good wine seller in your town, or perhaps in Manhattan, pack securely (and seal inside a couple of big Ziplock bags), and place in your checked bags around dark clothes that won't show wine stains in case of breakage. Or do what the other posters suggest, pack in Styrofoam or special packaging. I've done this before from JFK to SIN a few times, never had breakage (and all on UA, so two transits in between, thus three chances for something to get broken).

The STEB bag is used by duty free sellers on the secure side of an international airport. It's not something that would be available at a retail store - if I'm not mistaken, these bags are coded to a specific duty free retailer and are serial numbered. The question is (as asked by one poster) whether or not duty free at EWR supplies such bags. My presumption is yes, otherwise they'd be cutting themselves out of a bunch of sales. But then again, I could be wrong. This is what you need to find out. And even if EWR duty free does pack wine in such bags, it's hard to say what wine they'd sell. Thus my suggestion about purchasing from straight retail; knowing what you will buy is worth the sales tax and retail markup. As for purchasing from Japan Duty Free, not having purchased liquor from them, I suspect on a bottle to bottle comparison against US retail wine prices you won't be getting any bargains. Having said that, your 3+ hour transit time is more than sufficient to check out what they have to sell.

As for the import limits, no insult to the posters weighing in on Japanese limits but follow the limits for Indonesia. Alcohol limits for Japan are not relevant since you are only transiting NRT, you're not legally entering Japan unless you're planning to physically enter Japan (eg end up on say the bullet train to Tokyo with your wine). Excess liquids are being intercepted at a security checkpoint similar to (but more polite) than TSA between your two flights; they're only interested in liquids beyond the 100ml limit unless it's all in STEB bags.