If this was an one-off operation I'd do:
use DB;
show table status name where engine='innodb';
and do a rectangular copy/paste from the Name column:
+-----------+--------+---------+------------+-
| Name | Engine | Version | Row_format |
+-----------+--------+---------+------------+-
| countries | InnoDB | 10 | Compact |
| foo3 | InnoDB | 10 | Compact |
| foo5 | InnoDB | 10 | Compact |
| lol | InnoDB | 10 | Compact |
| people | InnoDB | 10 | Compact |
+-----------+--------+---------+------------+-
to a text editor and convert it to a command
mysqldump -u USER DB countries foo3 foo5 lol people > DUMP.sql
and then import after replacing all instances of ENGINE=InnoDB
with ENGINE=MyISAM
in DUMP.sql
If you want to avoid the rectangular copy/paste magic you can do something like:
use information_schema;
select group_concat(table_name separator ' ') from tables
where table_schema='DB' and engine='innodb';
which will return countries foo3 foo5 lol people