Salesforce Lightning Ready certification
I don't think you will need to worry about Canvas App being embedded in your visualforce for passing through lightning ready certification for your application .Since canvas app is essentially a mashup with external system,you don't have to match CSS with lightning design system .
For lightning Ready Certification, here are key things SFDC looks in your application :
Use SLDS Design Systems for CSS in your visualforce.This is mandatory .With Bootstrap I doubt you will be able to certify your app to lightning ready .There is significant difference in both Frameworks. SLDS uses SVGs for icons .
Test for supported browsers .(IE,Firefox,Chrome,Safari)
Make sure your app is responsive and at a viewport minimum of 1024px wide and a maximum of 1920px wide. Make sure that your app responds elegantly when the left-hand nav opens and closes
Do use the new Salesforce Sans typeface. It should not be accompanied by any other typeface, with the exception of your logotype.
Try to Align with Basic Page Layouts like salesforce Edit ,List view and Detail View on Lightning experience .
In short your App should be functional in Lightning Experience and the CSS should match as closely as possible to Lightning Experience .
Here is a little screenshot on how the badge looks for apps that are lightning ready and ones that are not.
