I'm the family cruise editor here. The following are some suggestions:
San Fran: Bay Area Discovery Museum: geared for kids two and up; sounds like there might be something for your child at the Tot Spot. Also take her to the waterfront/Fisherman's Pier to see the noisy seals. Lastly, she might enjoy a cable car ride.
Seattle: SEattle Aquarium might be fun for her to see the fish. There's also a Seattle Children's Museum -- check out the toddler area called Little Lagoon.
Vancouver: You could spend a whole day in Stanley Park. The Vancouver Aquarium is there along with beaches, playgrounds, horse and carriage rides, rose gardens, etc. It's a great spot for families.
Hope this helps. I'd love to hear from you after your cruise to see what you did do with y our toddler. I have a 16 month too as well as a 9 year old.
Smooth sailing,
Luisa Frey Gaynor