The estimated data is from the 2010 Census and can be sorted to easily find a particular city (if it was over 65,000 in population and had data available). While the average bike commute rate in 2010 in the U.S. is .53%, it represents a 40% increase from 2010. Only 'bike/walk-to-work' trips are listed - total biking and walking trips are much greater. Two spreadsheets are described and linked below.
"A look at the country's 70 largest cities shows that the communities that have done the most to promote bicycling through engineering, education, encouragement, enforcement, and evaluation – determined by the League's Bicycle Friendly America program – have seen greater increases in bike commuting over the past decade than non-Bicycle Friendly Communities.
Portland was highest with 6% commuting by bike, followed by Seattle with 3.6%, and San Francisco and Minneapolis at 3.5%.