Hi Dennis...
These are just a few suggestions that I have for that area:
I took a similar cruise last summer during the end of July and first week of August. It was the first week it hadn't rained the whole summer. I didn't do the land and sea cruise so I'm not sure if that is good or not. Some friends we have talked with said the land part was good and bad depending on the weather.
A few things to consider. It's more expensive for airfare flying in to Anchorage and out of another city than to Vancouver or Seattle. Second, IMHO, I would pick a ship that goes into Glacier Bay. They are restricting the number of ships that can go into Glacier Bay and that was our most beautiful scenery day on the cruise. It is absolutely stunning to see. Another suggestion is to take a seaplane tour over the Misty Fijords. This was my kids favorite activity.
As far as seeing lighthouses goes, I only saw one from the ship. Our ship went into Haines and we were able to go by Eldred Rock. There are not many ships going into Haines anymore.
As far as staying in Vancouver goes, I would leave there and take the car ferry over to Victoria. It is a beautiful city to stay in with lots to see and do. John and I stayed in a Best Western that was one block from the car ferry and right by the downtown water front. It was about $120/night but came with a continental breakfast. It is an easy drive to go see the Fisgard lighthouse while in Victoria. John and I also took a seaplane tour out of Victoria and flew over the San Juan Islands to see the orca pods. You can see Lime Kiln lighthouse from the air. This was lots of fun.
You can continue on down towards Seattle by taking the car ferry to Friday Harbor and overnight in the San Juan Islands. You can see Lime Kiln and Cattle Point lighthouses on San Juan Island. Continue on the car ferry and go to Anacortes. Drive down highway 525 and stop at Admirality Head lighthouse. The next ferry you take towards Seattle comes into dock right next to Mukilteo lighthouse.
There is so much to see and do in this area that it's hard to do it all in a couple of days. Most of where we stopped to eat was just finding a place that was on our route as we drove along so I don't have much to reccommend for dining. We did enjoy eating at the top of the Space Needle as it rotates around the city for some nice views.
Sorry this is so long.