This is pretty hard. Both have disappointed me in many ways and have surprised me in others. Capcom has been awesome at re-releasing downloadable classics and remaking them. Bionic Commando: Rearmed, Street Fighter II Turbo HD Remix, Mega Man 9, 1942: Joint Strike, Super Puzzle Fighter II. All great. Their DS offerings have been pretty decent, but not outstanding. Magaman ZX is pretty cool and so is Phoenix Wright. Their PSP reissues were also fantastic. Puzzle World, Street Fighter Alpha 3, Capcom Classics Collection, Ghouls and Ghosts, Mega Man Powered Up. Their console stuff though just hasn't impressed me very much. I've been overly disappointed all around.
Now for Konami. I love MLB Power Pros. I love the new Suikoden(outside of the abysmal voice acting). I love Contra 4. I love every Castlevania release and re-release. However, MGS4 was probably one of the most disappointing games I've played all generation. I'll just break it down by platform:
PSP: Capcom
PS3: Capcom
360: Capcom
DS: Konami
Wii: Capcom
As overwhelming as that looks in Capcom's favor, the DS is actually my lifeblood, so I give the edge to Konami.