I am at the end of my STD, Dr says I'm not ready to return to work and stated I should apply for CPP disability. My question is, do I apply for CPP disability first, or continue into the LTD claim?

You can do both at the same time. CPP Disability often takes several months to be approved, so you do have a bit of a wait for that money if you're approved.
Additionally, your LTD insurer will ask you if you've applied and will want to know if you're approved for this as they will get a credit for any CPP Disability you receive money. It can be a bit confusing, so I recommend you review our guide on the topic https://stlawyers.ca/disability-law/faq/cpp-long-term-disability/. If you still have questions, please reach out to our disability specialist, Rebecca, at rebecca.stap@stlawyers.ca and she can answer any further questions on this topic (at no charge!)