I prefer the pm trains, sometimes a little clearer weather with the mist burned off. But most important for first time visitors is a morning stop at the Park Service Visitor center- stopping here first will greatly enhance your later train ride. http://www.nps.gov/klgo/index.htm
I would then direct book the train for the $10 pp savings and board the train 2 buildings down rather than returning to the ship for the ship excursion boarding.
We would suggest the am train as the train is not nearly as crowded and it allows you to walk around a bit more and stand outside. One side of the train (the east side) is always hugged against the mountain, which only allows those on the opposite side the best view. Since the train never turns when it gets to the top of the pass, it just comes down backwards. As a result, it is requested by the train employees that people swap sides at the top of the pass so that those who didn't have the best view on the way up, have it on the way down. Taking the am trip increases the chances that you can have the best view both ways. As far as the weather is concerned, I am not sure if the weather is better at any particular time of the day. You will certainly enjoy the trip....It was our favorite part of our cruise on the Sky Priness two years ago out of San Francisco
The train was the only pre-booked tour that we did, and was well worth it. The evening train will certainly be less crowded than the afternoon one. When you get off the ship, you will find that certain carriageson the train are set aside for your ship only. Look for them when you get off. For the other ports, we like to rent a car in advance and do our own thing. That way you can do what the tours do, at a fraction of the cost.