The six-time Olympic gold medallist took almost a fifth of votes (19%) in the YouGov survey of more than 1,100 Scots.
Tennis star Andy Murray came second with 16% in the poll commissioned by National Lottery Good Causes.
Sir Alex Ferguson, Sir Jackie Stewart and Kenny Dalglish made up the top five best-loved sports stars of all time.
Murray clinched the greatest sporting moment however, with voters choosing his victory at Wimbledon this year as the most memorable ever.
Hoy's record-breaking sixth Olympic gold medal at the London Olympics scored second place.
Third most popular was Scotland's triumph against England at Wembley during European Championship qualifiers in 1967, followed by Archie Gemmill's goal against Holland in the 1978 World Cup.
In joint fifth place were Rhona Martin leading an all-Scottish curling team to take gold for Britain at the Salt Lake City Winter Olympics in 2002 and Scotland's rugby team defeating England to win the Calcutta Cup in 1990.
Cycling legend Sir Chris, from Edinburgh, said: "It's a great honour to be told that Scottish people think of me as a sporting hero. I hope that seeing Scottish athletes doing well has inspired people of all ages across the country to take part in different sports.
"I've been able to live out my ultimate dreams by winning medals at four Olympic Games and National Lottery funding was really important to me.
"It gave me access to facilities, coaching and medical care and allowed me to train full time when I graduated from university. I'm looking forward to the Commonwealth Games next year and seeing more Scottish athletes have the chance to shine on an international stage."
Vicki Kennedy, at the National Lottery Good Causes, said: "It's no surprise that Sir Chris Hoy and Andy Murray have topped these polls - they are a credit to the nation and have made it a fantastic time to be a sports fan in Scotland.
"As we look ahead to the Glasgow Commonwealth Games in 2014, I'm excited to witness more magic moments being created by young Lottery funded athletes such as Michael Jamieson and Eilidh Child."
YouGov surveyed 1,102 Scottish adults online between August 9 and 12.