Part of what makes Vancouver scenery so spectacular is the combination of water and mountains--the downtown peninsula is surrounded by English Bay (the Pacific Ocean), False Creek (the waterway that runs south of downtown), and the Burrard Inlet.
Boat tours and cruises are a wonderful way to experience Vancouver's outdoor beauty, especially on a sunny day (although they're still worth it in the rain, too). Most boat tours and cruises operate primarily from late April to October (the summer season, basically). If you are traveling to Vancouver between October and April, visit the official company websites for information on private tours/charters and special events. For example, Harbour Cruises offers boat tours of the Carol Ships Parade of Light in December. Non-tour options, like the Aquabus, run year-round.
Harbour Cruises is one of Vancouver's oldest city cruise companies, and it offers a wide array of tours. For travelers and sightseeing, their one-hour Vancouver Harbour Tour (late April through September) is a great introduction to Vancouver; it includes a narrated "tour" of the sights on the Burrard Inlet, as well as photo ops and views of the Vancouver skyline, North Shore mountains, and Stanley Park. They also offer Sunset Dinner Cruises (with dinner included) for the summer season.
In late July/early August, there are Fireworks Cruises, for viewing the annual Celebration of Light Fireworks.
The Vancouver Aquabus is not a boat tour per se; that is, it doesn't have a tour guide or any amenities. Rather, the Aquabus is a mini "water bus" for ferrying people around False Creek; many locals use the Aquabus to get from Yaletown to Granville Island (for example).
For visitors, the Aquabus is a very inexpensive way to see Vancouver from the water. Aquabuses run year-round in every weather and make eight stops around False Creek, including Science World. Start from Granville Island and hop on and off, or simply stay for the entire, circular route and treat it as sightseeing. Families with kids may prefer this option to an organized tour, just because it's so easy to hop off if you need to, and shorter than a cruise.
Like the Aquabus, False Creek Ferries are small boats that locals use to move around False Creek. Also like Aquabus, they're a great option for sightseeing on the water for cheap and allow you to stay aboard for the entire route or hop on and off.
Originating on Granville Island, False Creek Ferries stop at Vanier Park (home to the Museum of Vancouver, Vancouver Maritime Museum, and Bard on the Beach), Yaletown, Science World, and the Vancouver Aquatic Centre (one of the city's top indoor public pools).
While Harbour Cruises sail north of downtown Vancouver (on the Burrard Inlet), Accent Cruises' public summer Dinner Cruises leave from Granville Island, south of downtown, and sail northwest around Stanley Park, which means views of several Vancouver landmarks--including Vanier Park, Kitsilano Beach, and English Bay Beach--as well as the city skyline and Vancouver's famous bridges (Burrard Bridge, Granville Street Bridge, and Lion's Gate Bridge). Private charters are available year-round.
Accent Cruises are dinner cruises, rather than straight-up sightseeing tours.
Voted Best Boat Cruise in Vancouver in Georgia Straight's Best of Vancouver Awards 2014, the Summer (July - August) Salsa Cruises play "the best in Latin music on three levels of the largest cruising vessel in Vancouver, the MV Britannia." There are also special "family-friendly" day cruises, too.