Step 1: Identify tense and subject.
The sentence He rarely speaks in the class is in simple present tense, third person singular.
Step 2: Form the interrogative correctly.
For simple present with third person singular, we use Does + subject + base form of the verb. Speaks changes to speak. The frequency adverb rarely stays in the question.
Step 3: Confirm the answer.
Option (1) is correct. Options (2) and (3) use wrong verb forms, and option (4) incorrectly uses Is as the auxiliary verb.
\[ \boxed{\text{Does he rarely speak in the class?}} \]