A quick search of the Boston area water authority shows that they use a combination of methods to treat the water including ozone, U.V. and mono-chloramine, the latter which is a combination of chlorine and ammonia. I will assume this is the chemically created ammonia you are referring to, correct?
What you will need to use is a water conditioner that is labeled for use with chloramine treated tap water such as Seachem Prime (liquid) or Safe (powder) or another brand to treat the water you want to use to both fill your aquarium initially AND for all water that you add to the aquarium. Many people have the same issue with chloramine treated tap water and aquarium companies have created these type of products so that you can safely use such treated water in aquariums.
No need to use bottled water for the aquarium for a few reasons. One, it can become expensive and you have to transport it and two, it doesn't provide the minerals your fish need.
I hope this answered your questions but if not, post any more you may have. BTW, Welcome to C-F!!!