Two thoughts. I've received legitimate email from a registrar where I was listed as a contact for a domain. If no one uses an email address in your domain to register, that's not a problem.
And second, whois is the way I query to find out about a domain, answers to questions like who registered it, with which registrar, and when. It may be safe to query it directly, but I'm a chicken, when I decided to include whois reports for each distinct IP address that directed Heartbleed attacks at our servers, I rate limited the queries and cached the results.
