Sealing ported enclosure to reduce boom

I stuffed the port with polyfill. I guess if you completely cut off the airflow in the port the movement of the drivers will be compromised.
The ports are shaped like an "L" I think and are big (I can fit my hand inside). I don't know how I would be able to modify the port size without a lot of construction.
I haven't had this problem in this room (and in the same place) with other speakers (B&W, Polk, JBL, Infinity 7).

I had a pair of Dynaudio Focus 140s. They came with port plugs. I like the sound with them in better in my bedroom system. Just too much boominess without them. They sounded great with the ports plugged. And it was very easy to pull them in and out for experimentation though it was immediately clear to me that they were best left in for my setup.

"Sealing" the port is a bad idea. The drivers and crossover were designed to work with the port open, at least to some degree.

Knownothing, how would it affect the crossover?

Here's an example what you're effectively doing when a port is plugged.
http://yfrog.com/4jw26fxsealedvsportedj

Depends on the speaker, but if you have a three or more way speaker and multiple ported chambers, you could have some frequencies drop out if the mid woofer driver/crossover combo is "looking" to the port for bass reinforcement. Probably not common, but possible.

There is a very fundamental theory of room acoustics which no one has mentioned yet. Place the speakers at one of the room nodes and see how the boom reduces drastically. So how do you find out a room node ? It is simple, play a bass track which typically has an overhang in your room. Connect one speaker at a time (disconnect the other speaker). Stand next to the speaker that is playing, move around the speaker listening for the location where you hear the maximum overhang. You can just move within a radius of 1 foot form the existing location of the speaker and find out the spot of maximum bass/overhang. Once you locate it, place the speaker right at that spot. Repeat the same for the other speaker. You may have to move them inches to get the right imaging but for sure your bass issues would be reduced. You may even do this for one speaker, which you think is causing the maximum boom, this also you can ensure by playing a single speaker at a time and listening from your sweet spot to determine which speaker is causing more boom. Do it for that speaker, keep it fixed at that location and move the other speaker around for imaging and staging. Try it !!