I wrote a simple AppleScript that does it.
tell application "Numbers" activate tell the front document tell the first sheet set original_range to selection range of first table set orignal_table to first table set number_of_columns to column count of orignal_table set number_of_rows to row count of orignal_table set trasposed_table to make new table with properties repeat with i from 1 to number_of_columns repeat with j from 1 to number_of_rows tell orignal_table set original_value to the value of cell i of row j end tell tell trasposed_table set the value of cell j of row i to original_value end tell end repeat end repeat end tell end tell end tell
Here you can find more details about it.