World History

The largest U boats were the Type X B mine layers. Several were used to transport items to Japan. http://www.uboat.net/types/xb.htm

They had an overall length of about 278' and a beam of 28' 6" external but only 14' 8" internally.
It is conceivable these subs could transport either V-1s or V-2s. Launching would be an entirely different matter. The sub would have to surface, construct the missile then launch it. It would be extremely difficult.
Germany built 8 of these boats and all were accounted for with no gaps in their war records indicating such a secret mission.

The Type XIV supply boats would be another candidate. There is anecdotal evidence that one or two may have had trial ramps installed for launching V-1s but no conclusive proof of this.

By comparison, the purpose built Japanese I-400 class could carry and launch three seaplanes. They were 400 ft long and could launch all three planes in 45 minutes.
http://en.wikipedia.org/wiki/I-400_class_submarine