We did the "Off the Beaten Path" cruisetour 5 years ago, and loved it! Haven't looked at the current offerings, but it ws 14 nights total. Started in Anchorage, went to Copper River (2 nights), Fairbanks (2 nights), Denali, and Mt. McKinley, before the Southbound cruise out of Whittier. There were two long bus days, broken up with stops, and the train from Denali to Talkeetna. Copper River was definitely our favorite lodge! We did a la carte meals, and took advantage of two local restaurants in Fairbanks. This tour also did the excursion on the Chena River (including the replica Athabaskan village) and the Gold Dredge - touristy, but enjoyed it more than I thought I would. The Natural History tour in Denali was also included. I second the recommendation to do the land portion first!
Maybe, if we ever can go back to Alaska, I'd try the Rail Tour...