Susie,
I am sure 540 flies between Zanzibar and Mombasa. I was recently quoted US$209 as a promotional return fare when I contacted them (I didn't book it). It might still be on offer, but the specials don't always show up on their website - you need to contact them.
540 seems to offer the cheapest fares on this route of all the airlines.
Mombasa-Dar buses leave early every morning from the middle of Mombasa. There are various companies but they all have booking offices near the Kobil station on Mombasa Rd. The fares start from around 1,300 Kenya shillings and go up from there.
The buses drop you at the Ubungo terminal on the outskirts of Dar, so you need to get a minibus or taxi to cross the city to the Zanzibar ferry dock. The bus is supposed to reach Dar in time for the last ferry in the afternoon, but don't bank on it.
The newest, fast Zanzibar ferry now costs US$40 each way! However, there is a cheaper alternative called Flying Horse for $20 each way. The only problem is that it leaves around noon (it is an overnight ferry coming back from Zanzibar).
Considering all that, you may find it better to fly. The 540 fare isn't much more than the costs of all the buses and ferries put together.