Great question — answering as the UphillTech team:
I will try to be precise in my answer: I can not see how a domain ranking for a city could affect (or cannibalize) the other two websites with different locations. The only possibility I can think of is about the way the boston website is organized, webserver location and configuration, Website NAP, number of website backlinks from local business directories, Map listings and any other signal that strongly suggest your website is serving a region or delivering content to that same region. I would suggest to use a moderate approach, an strategy that will take sometime before seeing results. Do not to change your boston.com site as it is ranking. If it is possible create a separate website...
Full answer by Raul Reyes: https://webmasters.stackexchange.com/a/109756 (CC BY-SA 3.0).
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