It's definitely possible if the tables are somehow related. A free-form query can be used in Sqoop to do exactly that. In this case, the free-form query would be a join. For example, when importing into Hive:
sqoop import --connect jdbc:mysql:///mydb --username hue --password hue --query "SELECT * FROM users JOIN customers ON users.id=customers.user_id JOIN employee ON users.id = employee.user_id WHERE \$CONDITIONS" --split-by oozie_job.id --target-dir "/tmp/hue" --hive-import --hive-table hive-table
Similarly, for Hbase:
sqoop import --connect jdbc:mysql:///mydb --username hue --password hue --query "SELECT * FROM users JOIN customers ON users.id=customers.user_id JOIN employee ON users.id = employee.user_id WHERE \$CONDITIONS" --split-by oozie_job.id --hbase-table hue --column-family c1
The key ingredient in all of this is the SQL statement being provided:
SELECT * FROM users JOIN customers ON users.id=customers.user_id JOIN employee ON users.id = employee.user_id WHERE \$CONDITIONS