In total your questions are difficult to answer, in part because most of us are only licensed to practice in one state so our knowledge will be concentrated on that state.
Any way lets try slightly out of order
Commuting - I worked on Wall Street and commuted from New Jersey for 20 yrs so I am an old hand. Before that i lived on Long Island and comparing the 2 I would pick New Jersey. Most of Bergen County is close enough to qualify as would Essex county. I lived in Montclair for 10 years and from my house to the World Trade Center was a little over an hour.
Both counties have a web of train lines and express buses although if I am working on Wall Street i am going to prefer the train into Hoboken as the bus wi8ll bring you to the Port Authority in Midtown.
Environment - The tri sate area is very crowded so its almost impossible to be perfect. However with carefull planning you will be far enough away from highways and there is not much industry remaining in the area.
Taxes are going to be high everywhere but did you know your target of $18,000 would cover a house of up to $2,000,000 in a couple of towns but in general would certainly have a ceiling of $1,000,000
Schools In Bergen county a house of $1,000,000 would guarantee you some of the top schools in the state if not the country. the magazine New Jersey Monthly (google it) publishes an annual report of all the high schools in the state with SAT's AP courses and so on.. trust me schools are the least of your worries.
As far as flood zone is concerned through the Mls I have access to the flood maps and before I show a house to anyone I make sure that I check .
To sum up any one of more than a dozen towns in Bergen County would work for you. If you go to my web site there is a search engine there for you to search out towns.Pick a few and we can provide you with detailed information on the items that concern you