We've stayed CL at both CR and BC and they are very different, so it's difficult to say which is best. Overall, we prefer BC, but we really like the CR CL lounge. A few comparisons might help:
Lounge: CR's lounge is much more spacious and the view of MK is absolutely amazing. We loved having a bay lake view from our room (peaceful, quiet) and the MK view from the lounge (fun!) Huge windows in the CR lounge and some of the friendliest CMs we've met on Disney property. Just love how open the whole space is. I think the CL lounge at CR is outstanding, and was really the highlight of our stay there. Not sure we'd enjoy CR as much without the club lounge. BC's lounge is definitely smaller and doesn't offer a view. We prefer the food in the BC lounge, but only by a little bit.
Rooms: CR rooms seem bigger, and are well decorated - really clean lines and comfy beds. I love the sliding glass doors out to the patios. But the air conditioning is a little louder and you can see a few signs in the corners and on the ceilings that remind us CR is a Disney original. We don't mind - they've done a great job updating a Disney classic. I prefer the theme of the BC rooms and I also prefer a 5-story resort over a high rise generally. I find the balcony more relaxing at BC because we're not SO high up and the overall environment is more quaint. Not all BC rooms have full balconies (some are juliet), so you'd need to request that if it's important to you.
Pools: BC wins - no question for us.
Dining: Again, BC wins for us because of its proximity to all the wonderful Epcot and Epcot area dining options. No waiting for monorails or buses - just walk!
Location: If you're spending lots of time at MK, can't beat walking there from CR. But we tend to spend the day in one park (MK, DHS or AK) and then go to Epcot for dinner. So BC is far more convenient for us. We stayed at CR last year for
MNSSHP, which was really convenient for that particular purpose. But for most trips, the BC location works better for us.
Transportation: As I mentioned, we loved walking to MK from CR. But for DHS, it's a bus and for Epcot, it's a monorail to TTC, switch monorails, and then get to Epcot. For us, that's not as convenient as BC, where we can walk to both Epcot and DHS (or boat) and bus to MK. It's bus to AK for everyone, so we don't usually include that in the analysis.
Resort grounds/area: BC wins for us because we love to walk and when we stay in the Epcot resort area, we have access to BC, YC, BWI, Swan and Dolphin - so there's quite a lot around. Not enough walking area for us around CR and far less theming, so we prefer BC.