It looks like you have a lot of moving parts there.
The conforming limits for 3 family homes in Boston is $720,700 and for FHA is $810,450.
From a down payment standpoint, you're probably looking at needing at least 20% - either to meet the conforming/FHA loan limits and qualify for better rates OR to qualify for jumbo financing options.
I don't know of any portfolio options with less than 20% down, primarily because PMI is not obtainable over the FHA/conventional limits.
I can help you in reviewing your options if you want to give me a call or shoot me an email.
Loan Officer -NMLS #966417
WCS Lending, LLC
Toll Free: 866.936.5363 ext. 278