One of several companies operating boats along the River Thames, Thames Clippers offers proper commuter services. It's fast, pleasant and you're almost always guaranteed a seat and a view. Boats run every 20 minutes from 6am to between 10pm and 11pm. The route goes from London Eye Millennium Pier to Woolwich Arsenal Pier, with boats west to Putney, too.
Boats serve the London Eye, the Tate Modern, Shakespeare's Globe, Borough Market, Tower Bridge, Canary Wharf, Greenwich and the O2. Discounts apply for pay-as-you-go Oyster Card holders and Travelcard holders (both £6.60).