BVB was assured of first place in Group D a fortnight ago, Schalke secured top spot on Tuesday night, and then Bayern beat BATE Borisov 4-1 on Wednesday to finish ahead of Valencia in Group F with 13 points from six games.
"All [three German teams] deserved to win their groups. It's nice to see that the Bundesliga is alive and catching up with the very best leagues," Gomez was quoted as saying on the UEFA website.
"In terms of strength across the board, I'd even say it's the best at the moment. The top teams are all performing strongly in Europe."
No German team has won the Champions League since Bayern beat Valencia after penalties in 2000-01, but the nation will be hopeful of European success this term with three teams among the final 16.