Haven't been on enough boats to really comment on which ones are good and which ones are less good for birding.
However, what perhaps is more important are the islands you visit. For example; not all boats visit the western coast of Isabela or Fernandina and without one of those, the chance for the Galapagos (Flightless) Cormorant is zero.
Likewise, not all boats visit the island of Española and that's pretty much the only place where you can see the Hood Mockingbird (luckily, it's common & very tame, so even a short visit to Española will usually result in sightings of the Mockingbird - I've even had one checking between my toes for food!). That's also the island where the Waved Albatross breeds and unless you're lucky and see one out at sea, Española is pretty much your only chance. Española is also your best chance for Large Cactus Finch as few boats (except diving cruises) visit the far away islands of Darwin, Wolf & Genovesa where it also occurs.
For the Medium Tree Finch you'll need a visit to Floreana (another island not all boats visit) and your best chance for that species are the highlands, which unfortunatly only are visited on some tours.
The Chatham Mockingbird is easy on the island of San Cristóbal, but that's another island not visited by all boats.
Sharp-beaked Finch is easy on Genovesa (and probably also on Pinta, Darwin & Wolf), but none of these islands are commonly visited, except by birding or diving tours. It can also be seen on Fernandina and Santiago, but as you only can visit former from the sea-side and tours only rarely visit the highlands of the latter, chance on both would be very small
Unless going on an actual birding cruice I'd recommend a few days on one of the hotels in Puerto Ayora (on the island of Santa Cruz), where it is easy to arrange for short visits by car to the highlands. Most of the more widespread Darwin Finches (Large, Medium & Small Ground, Common Cactus, Vegetarian, Large & Small Tree, Woodpecker, Warbler) and the Rail are not really difficult, but some of them do require more time e.g. in the highlands than usually spend on an ordinary tourist boat. Likewise, some of the Darwin Finches can be difficult to ID, making it easier if you can do it at your own speed, rather than being rushed through with "ordinary" non-birding tourists. Don't expect the guides on the ordinary birding tours to be able to recognize all the Darwin Finches. Sure, he/she probably can recognize many of them, but for the harder ones you're likely to be on your own. The Galapagos Rail (restricted to the humid highlands) is easier than most rails of the South American mainland, but bringing a tape with its voice still will be of great help (the voice can be found on Hardy, Reynard & Taylor's "Voices of the New World Rails" - available through wildsounds.com and probably elsewhere too). So, a sum-up:
* W. Isabela: Galapagos (Flightless) Cormorant. This is also your best bet for the Penguin, although it also can be seen (in much lower numbers) elsewhere (e.g. Bartalomé).
* Española: Waved Albatross, Hood Mockingbird & Large Cactus Finch.
* Floreana: Medium Tree Finch (mainly in the highlands and thus easily missed - chances for a lowland encounter is probably highest during the dry season ~ May-Dec).
* San Cristóbal: Chatham Mockingbird.
* Genovesa: Sharp-beaked Finch. An island not commonly visited, except by birding tours and diving tours, but you may be lucky. With lots of luck perhaps also possible during the dry season (~May-Dec) on Santiago, but at other times restricted to the rarely visited highlands on that island.
* A few days in Puerto Ayora (Santa Cruz) to pick up any of the more widespread Darwin Finches & Galapagos Rail missed on the boat-tour.
The three "top" sites in my opinion would be W. Isabela, Española & a few days at Puerto Ayora (for the Santa Cruz highlands). This combination would likely also result in the highest number of endemics (ok, W. Isabela only really gives one endemic not possible elsewhere - the Cormorant - but it is worth the relatively long trip).
Galapagos Martin & the distinctive galapagoensis Short-eared Owl are hit and miss birds. They can be very easy or they can be very hard; depends on your luck. However, unless going on an actual birding tour the chance for the highly restricted Mangrove Finch and Charles Mockingbird are small. On my first tour to the Galapagos I actually did manage to see the latter from an ordinary tourist boat when we sailed past Champion (it is no longer found in Floreana itself, but is restricted to the small islands of Champion and Gardner, both situation near Floreana), but that was clearly good fortune. I'd suggest you start collecting info on the Darwin's Finches... some of those ID's can be tricky and hybrids do occur.
In regards of a "good forest lodge" in mainland Ecuador you'll have to be more specific. There are many kinds of forest in Ecuador (Chocó, east slope, Amazon, etc.), each with unique birds.
