Your question sent me off to read about the history of marijuana smoking in England, though I haven't found much reliable information. From Wikipedia I could find a study, prompted by certain phrases used by Shakespeare in the 16th/17th century, finding traces of cannabis in pipes buried in Shakespeare's home town:
Why write I still all one, ever the same,
And keep invention in a noted weed,
Shakespeare, Sonnet 76
However, even if this does indicate that marijuana consumption wasn't unknown in England before Carrol's days (which it does very weakly) it still doesn't imply that Lewis Carrol himself smoked marijuana (despite extremely flaky claims such as the fifth paragraph here), or that he was familiar enough with the habit to insert it into his rather hallucinogenic fantasy world.
Some googling for "lewis carrol marijuana" and variants thereof led me to many "Was Lewis Carrol advocating marijuana usage?" pages, but nearly all were on marijuana and cannabis advocacy sites that don't even try to present any evidence (see here or here).
In short, since tobacco smoking was well-known and popular in Victorian England, and the hookah was becoming known after the conquest of India, I see no reason to assume cannabis was in the caterpillar's hookah.
That is not to say that evidence for other hallucinogenic drugs can't be found. This is just my 15 minutes' worth of research. :)