Our crawler (https://www.apify.com/docs/crawler) currently runs on PhantomJS, while Actor (https://www.apify.com/docs/actor) can run arbitrary jobs, including jobs that use headless Chrome and/or Puppeteer - for example, see https://www.apify.com/docs/actor#examples-puppeteer
BTW we're working on migration of Crawler to headless Chrome.
If you could provide more details about your use case, I'm sure we will figure out how to do it with Chrome.