"Had" is the past tense of the verb "to have", and this sentence is written in past tense, therefore "had" is correct. Also, "has" would not be correct here anyway - in the present tense, you would say "I have, you have, we have, they have" or "he has, she has, it has." Because the speaker says "you boys", you would use "you boys have" instead of "you boys has".

Well, the least I could do WAS make sure you boys had a decent meal to look forward to in the morning. Because it is all in the past. Well, the least I couId do is make sure you boys HAVE a decent meal to look forward to in the morning. This is also possible, since "could" can be either past or present. But watch out for the is/was!

"Had" is conjugated in the past tense. "Has" would be a third person singular, present tense conjugation.

I agree with Lauren: it's a sentence in past tense, and "could" is your clue. "Well, the least I couId do is make sure you boys had a decent meal..." Compare this to the present tense version: "Well, the least I can do is make sure you boys have a decent meal..."