Shuls and Yeshivas ARE bad neighbors, but not because of the Shuls or yeshivas themselves, but the traffic, double parking and congestion around davening times.
People who will walk 5 blocks to shul on shabbos, will drive during the week and take up all the parking spaces the people who live on the block need.
NYC is a sense of scale. Its a very large city and small increases arent a big deal to it. 20,000 people (Just a random number) isnt a big deal in a city of 8.5 million. However its a very big deal in a county of 400,000
The other problem is Taxes. Religious institutions dont pay property taxes. NYC has a large corporate tax base so its not really an issue. A small shul on 46th St in Borough park doesnt make a difference in NYC. it a big deal in Monsey where there are very few corporations to make up for theloss
edited a bit