I made this move in the other direction back in 2010. My main gripes about Boston are the weather! Seattle weather is great in comparison. :)
We used a pod, it worked out great. If I had to move cross-country again, that's how I would do it.
In Seattle, you find an apartment a week before you move in. In Boston, you find an apartment 3+ months before you move in. That was a bit of a shock to us, as we actually took a trip to Seattle 2 months before moving to find a place to live, but no one was advertising places for rent that far out. So definitely get your housing situation sorted out before moving out there. Worst case, find some friends who are looking for a housemate situation; live there while you search for your own place.
I've never used an agent to find a place to live - Craigslist always worked just fine. That said, we rented our condo out for a few years using an agent, mostly because we were able to charge more for rent. The people using agents tended to be willing to pay more for rent.
Living on the Red Line (in Somerville/Cambridge) is the way to go. I lived in Davis and Porter, and they're both wonderfully walkable, friendly, and _dense_. You'll meet friends/coworkers who live just a few blocks away, which makes it incredibly convenient to hang out with them. On the flip-side, we almost never visited friends who lived in Brookline, because the Green Line was so awful. Biking there was kind of a pain, too (not in terms of distance or hills, but in terms of the unfriendly roads and drivers). Boston proper is kind of dirty and gross; a friend who lived there always had black soot forming on his windows from the cars.
If you're looking for really cheap rent, check out Arlington or Lexington. The 77 bus runs every 5-15 minutes, and goes to Harvard Sq (Red Line). It's also along the Minuteman Trail, which is great for biking. I lived in Arlington Heights, which was where the 77 ended, and right next to a Trader Joe's. Since the buses waited at that bus stop, rather than having to wait in the cold, I could just hop right on the buses that were waiting for their scheduled departure time. There are probably other gems like that out there, if you're willing to live a little further out.
Don't live so far out that you need to rely on the commuter rail. It sucks (that's all I'm going to say about that), and the temptation to just get a car will be too great. Also, don't work out there. I had a job in Burlington for a while, which was awful to commute to; the bus only came every hour, and was slow.
At the time I was living there, the cost of housing was cheaper than paying rent. I suspect that was due to the high number of college students who absolutely needed rentals, and had no interest in buying a place since they were only there for a few years.
Good luck!