Looking over the Boundary Waters on the terrain map, it looks like there are some large ridges and even peaklets. Do y'all know if there are any reasonably prominent peaks? Has anyone even been to the Boundary Waters?

Eagle Mountain is in the BW, it's Minnesota's highest point at 2,301'. Around that are the Misquah Hills, some other big hills.
NE of there, around Kiskidinna Lake is a pretty rugged area, and off of the Arrowhead Trail, around Pine Lake, and East & West Pike lakes are some quite large (for MN) hills.
Eagle Mtn is a cool hike, good views, etc, with a good trail.
Hiking off trail in most of the rest of the BW is not a whole lot of fun to me, LOTS of bushwhacking, etc.

Edit to add that the Border Route Trail, which goes through the last place I mentioned, would be a very cool backpack trip.

I honestly had no idea that Eagle Mountain was in the wilderness area. I am an idiot.

Planning a trip there?

Here is the view from just below the top (summit if you wish ) of Eagle Mountain. I've never really heard about any specific high points in BWCA outside of Eagle. Carry canoe up hill...paddle. Carry canoe uphill....paddle. Carry canoe uphill....paddle. That's portaging for ya.