While the Player's Handbook skill Handle Animal covers some magical beasts, it doesn't cover the cloud ray; the Epic Level Handbook's skill Handle Animal covers that (albeit poorly)
The Player's Handbook on the skill Handle Animal the in the Special entry says
You can use this skill on a creature with an Intelligence score of 1 or 2 that is not an animal, but the DC of any such check increases by 5. Such creatures have the same limit on tricks known as animals do. The Monster Manual provides information on teaching or training other kinds of creatures as appropriate. (75)
Thus, for example, a griffon (Monster Manual 139-40), a magical beast, has the note Training a Griffon, so griffons can be trained using the skill Handle Animal. (Note that applying the Player's Handbook's Handle Animal rules for rearing and training generally to all creatures with Intelligence scores of 1 or 2 probably wouldn't hurt anything.)
However, any character can take a full-round action to make a Handle Animal skill check (DC 30) to "push" an Intelligence 1 or 2 creature to perform on its next action a trick it doesn't know. This is probably an inefficient use of actions on the part of any character who can make such a roll, but it's a get-by until the creature can be trained.
Because there's no Training a Cloud Ray entry, according to the Epic Level Handbook on the skill Handle Animal on page 41, a cloud ray (Monster Manual II 49-50), with its whopping 30 Hit Dice, requires a trainer to spend 2 months and make a Handle Animal skill check (DC 70) to teach that cloud ray a lone trick.
Alternatives to the difficult and time-consuming Handle Animal skill check needed to teach a cloud ray a trick
If that strikes your table as, perhaps, a tad too challenging or a bit time-intensive, there are alternatives.
- The feat [Creature Type] Trainer (Arms and Equipment Guide 73) allows the character to pick a type of creature when the feat is chosen and use the skill Handle Animal to rear and train such creatures if the creature's Intelligence score is 4 or less.
Races of the Dragon on the skill Handle Animal says that
You can use Handle Animal to handle, train, and rear draconic animals, but since such creatures are magical beasts, you take a −4 penalty on the check to do so. Animals and magical beasts with the half-dragon template can’t normally be affected with this skill. (97)
Further, the feat Dragon Trainer in its Normal entry says
Without this feat, only animals and magical beasts with Intelligence scores of 1 or 2 can be handled and trained with the Handle Animal skill, and using Handle Animal on a magical beast is done with a −4 penalty on the check. (98-9)
It's likely Kestrel, Wilkes, and Liquette internalized their house rules on rearing and training magical beasts using the skill Handle Animal to such a degree they'd forgotten this rule was, in fact, a house rule (likely adapted from similarly penalized wild empathy checks). However, it's a good house rule, being extremely simple, easy to implement, and, for example, not requiring months of work on the part of all but the most optimized trainer to train a cloud ray.
Note that in this case Races of the Dragon contradicts the Epic Level Handbook, so if your table is strict and considers the Epic Level Handbook a primary source, the Races of the Dragon rules should be unavailable.