Brooklyn (non-Williamsburg) while getting pricier is still afordable. Without kids I'd recommend Clinton Hill area (schools suck there). If with kids, South Slope is a recently gentrified version of pricey Park Slope (where the Mayor lives) which hasn't quite caught up with Park Slope prices yet. There's also a bunch of commuter towns all around NYC in NJ that can guarantee sub-1hour commutes to Midtown where 1 bedroom can be had for 1200 or so with all of the aforementioned amenities.
Yeah, if you're not living next to a PATH train stop or the Secaucus train station, I would assume +30min of travel time to any day's commute. That kind of variance basically means your weekdays are spent going to work, coming home, eating, and going to sleep. Terrible. And you get to pay ever increasing NJ Transit fares and property taxes for it.
So obviously everyone's situation is different. I agree that NJT is a cluster$#% of epic proportions. In my case I'm in Montclair, around 12 minutes from an NJT station but around 1 minute from Decamp Buses which is what I take every day. I take the downtown Wall Street bus a block from my house at 6:50 AM and it drops me off near the bull at 7:50. The bus takes around 25-30 minutes to get to Port Authority and around around 20-30 minutes to traverse to downtown (people request stops). This year it's only been late (i.e. 8:10-8:20) to Downtown twice. One of those times was when major roads in TriBeCa were closed because of mailbomnbs. That's how rare of an occasion that is. Of course that's an early bus, later ones are subject to traffic variations.