Criteria are as follows:
1) Playing a high level at both. Not included are going to be people who were good as prepsters but chose one sports over the other and never competed in college or beyond.
2) Accolades at the higher levels: Halls of Fame, All Stars, playing on title teams, big games, achievement over just playing
These were all off the top of my head (little research done, except after the candidates were identified) so I might have missed someone. Feel free to set me straight!
So without further ado, the Top 5 two-sport athletes in Football and Basketball are below. Tends toward big men, tight ends for sure, with one major exception.
#1 - Charlie Ward
College: Florida State
Highest Football: College (Quarterback)
Highest Basketball: NBA (Point Guard, 11 seasons)
All Star season (Pro): None
Honors: Heisman (1993), Davey O'Brien (1993), All American (football, 1993), College Football Hall of Fame (2006), 1st round NBA pick, 2 time ACC athlete of the year (1993, 1994).
Records: Career and single game steals for FSU (basketball),
Championships: College Football National Championship (1993), Played in one NBA Finals (1999)
Comments: Best player in college football AND 1st round NBA selection goes a long way. His FSU basketball teams made deep NCAA tournament runs. NBA career was nondescript, but played for over 10 years. Was also drafted in baseball twice (despite not having played since high school) and was a noted prepster tennis player.
Highest Football: NFL (Tight End, 16 seasons, still active)
Highest Basketball: College (Forward, 3 seasons)
All Star season (Pro): 12x Pro Bowl, 9x All Pro (both football)
Honors: All American (college football, 1996), NFL All Decade team (2000's), NFL Hall of Fame (5 years from retirement), 1st round NFL pick
Records: Career receptions, TDs, and yards for a TE (NFL), single season receptions for a TE (NFL), consecutive starts for a TE (NFL)
Comments: If his college basketball career had been a bit more than just normal, he's by far the best pro on this list. One of his Cal hoops teams made a Sweet 16 run. By most counts, the consensus best Tight End of all time in the NFL.
#3 - Julius Peppers
College: North Carolina
Highest Football: NFL (Defensive End, 10 seasons, still active)
Highest Basketball: College (Forward, 2 seasons)
All Star season (Pro): 7x Pro Bowl, 5x All Pro (both football)
Honors: All American (college football, 2001), Defensive Player of the Year (2004), Defensive Rookie of the Year (2002), NFL All Decade team (2000's), 1st round NFL pick (2nd overall)
Records: Most Career Sacks (Panthers), Longest INT return for a Defensive Lineman (NFL, 97 yards), 2nd most blocked kicks (NFL, 12)
Championships: Played in one Super Bowl (2003)
Comments: Similar to Gonzalez, just not quite enough on the basketball side, although he played in a Final 4 and was heavily recruited by Coach K at Duke, but wanted a football path that UNC offered him.
#4 - Antonio Gates
College: Kent State
Highest Football: NFL (Tight End, 9 seasons, still active)
Highest Basketball: College (Forward, 4 seasons at 4 schools)
All Star season (Pro): 8x Pro Bowl, 5x All Pro (both football)
Honors: Mr. Basketball Michigan (runner up 1999), NFL All Decade team (2000's), Honorable Mention All-American Honors (Kent State basketball, 2003), Kent State basketball jersey retired (44)
Records: None (has the unfortunate position same as Kellen Winslow for franchise records).
Comments: Originally enrolled at Michigan State to play hoops for Izzo and pigskin for Saban, but Saban demanded his full attention for football. Transferred to Eastern Michigan and some JuCo until landing at Kent State his last 2 years. His Senior Kent State hoops team reached the Elite 8, upsetting Oklahoma and Alabama in its wake. Did not play football in college.
#5 - Jimmy Graham
College: Miami (FL)
Highest Football: NFL (Tight End, 2 seasons, still active)
Highest Basketball: College (Forward, 4 seasons)
All Star season (Pro): 1x Pro Bowl, 1x All Pro (both football)
Records: Briefly held record for single season receiving yards by a TE (broken later that day).
Comments: His career still young, yet to get many accolades, was not a star in college at either sport. Played 4 years of hoops at Miami, then played one last year of football after graduating with two degrees (marketing and management).
#5 Donovan McNabb (addendum)
Highest Football: NFL (Quarterback, 13 seasons, not yet retired)
Highest Basketball: College (Guard, 2 seasons)
All Star season (Pro): 6x Pro Bowl
Honors: 3x Big East Offensive Player of the Year (1996-8), Big East Offensive Player of the Decade (1990's) Syracuse All Century Team (20th), 5th in 1998 Heisman voting, 2nd overall NFL Draft pick (1999), NFC Offensive Player of the Year (2004),
Records: Eagles' leader career wins/attempts/completions/yards/touchdowns
Championships: NFC Champions (2004)
Comments: Also ran track and field and played volleyball in high school. Was high school hoops teammate with Antoine Walker (Kentucky). Played for NCAA Runner Up basketball team in 1996 (team lost to Kentucky and the aforementioned Walker), did not play in Final Four (Boeheim kept a 7-8 man rotation). McNabb did log time in the Sweet 16 round.