오늘은 시간이 돼요?  or 오늘 시간 돼요? 

adding 은 after 오늘 implies that the other person is not available on other days. 

Just casually asking the other person without further context is 오늘 시간 돼요? 

이 after 시간 is not necessary, but I just wanted to show that 을/를 can't be used here. 을/를 is only used with transitive verbs.