Chris,
I work for one of the largest Mass Housing lenders in the state, so maybe I can shed some light here:
Mass Housing is an awesome program. 3% is their minimum down payment on single families, but that jumps up to 5% for multis, usually with no mortgage insurance. Keep in mind that the mortgage insurance is essentially built into the interest rate, which is why it might look a bit higher. However with FHA, your mortgage insurance is not only expensive (1.35% of loan amount), but it lasts for the LIFE OF THE LOAN. So regardless of equity position, you will have mortgage insurance, unless you refinance.
Like others have mentioned, Mass Housing has income limits, and you must be a first time homebuyer. The income limit for Worcester County right now is $107,460 .
There is also first time home buyer education requirements, and if you are buying your first multi, there will be a landlord education requirement as well. The good thing is most of these classes are offered online these days.
You mentioned that MA Housing also allows you to use 65% of rents on a triplex to qualify, keep in mind this is only if the units are occupied at the time of purchase. If they are vacant, you can use 50% of the market rents set by the appraiser. With FHA, you can acutally use 85% of the market rents to qualify, another big reason why people choose FHA.
Feel free to contact me anytime if your looking for more info or want to know if you might be eligible.
Thanks,