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Is your Marketo User not seeing certain groups of records?
Did you delete some records in Marketo only?
Same thing shows for us. The big difference is in converted leads in SFDC. When our leads are converted into contacts in SFDC, there is only one record, the contact. However, when running a lead report in SFDC, it will still show the converted leads. Run a lead report in SFDC with "converted = false" criteria. That brought our count to nearly identical.
I've run into this with my clients before. Both what Josh and Nicholas said was accurate. I'd add in one more troubleshooting step:
In Marketo go to Admin -> Salesforce and find out who the sync user is between Marketo and Salesforce.
Log in to Salesforce as that user and see what records are visible. Only records that are available to the sync user will be visible in Marketo.
Nicholas: That worked for me! Our count's now only off by around 3-4, which isn't a worry.
Thanks for the tips, Jordan & Josh!
Great to hear!