The verb "haben" is conjugated as follows in its present simple tense form:
Ich habe ( i have)
du hast ( you have)
er/sie hat ( he /she has)
Wir haben ( we have)
Ihr habt ( you have)
Sie haben ( They have)
Verb 'haben' after "Ihre Augen" will be exactly conjugated like with the pronoun 'sie' in plural.
Sie haben (they have)
Ihre Augen haben ( your eyes have)
So it is:
Welche Farbe haben Ihre Augen?
If it was "Ihre Tasche" as a singular noun , the sentence would have been formed as follows:
"Welche Farbe hat Ihre Tasche ?"
Here, "ihre Tasche" is treated like the third singular pronoun (it/she/he)
It is like in English you can say:
"Your eyes are " but you can't say :
"Your eyes is "
Your example is of course an interrogative sentence and the same applies with a different sentence order :
(haben Ihre Augen) instead of (Ihre Augen haben)
I hope it is clear now :)