I just returned from 6 weeks in Cambodia, Vietnam, Thailand and Laos. Would you have the time, budget and energy to do a cruise, from say Siem Reap to Ho Chi Minh (Saigon is only one small area in HCM City), then pick up a land tour that goes up Vietnam to Hanoi (or reverse leaving the more relaxing cruise to last)? I did trip all by land, but with day boat trips. The Mekong and its Delta would be lovely to visit by a boat, but it is quite different to the rest of Vietnam.
I used a Vietnam company for my Cambodia/Vietnam portion (Legend Travel Group). Local agents may advertise group tours, but know they are not escorted tours as we know from North America. In so many ways I like them better, as you can do a little personalizing on them, and some time they are private, other days may be with other folks. They get you to airports for internal flights but you do the flight process yourself...and they meet you on the other side. So guided, but not escorted. Easy peasy. I wasn't expecting non escorted, but once I got my head around it, I really liked it. We tended to stay 2-3 nights in any one place and there were levels of accommodation to choose. I suspect most would prefer the 2 or 3rd upgrade option, though the basic level was adequate, clean, working AC, hot water and elevator. They will also build a private tour, which may be cost effective with 2 of you.
If this may be your only trip to Vietnam, I personally think just the south as a cruise would be short changing all that the country has to offer.
Take a look at Trip Report forum. There is a detailed report posted this month. Primarily for Vietnam with a side trip to Cambodia.