Yes, you can file as married filing jointly even if you did not make the estimated payments related to your self-employment income. You will be able to pay all the income and employment taxes related to your self-employment business with your personal tax return (if you are filing a Schedule C for your self-employment business).
If you decide to make an online estimated payment on Jan 15th, 2018 that applies to your 2017 self-employment income, you will be able to add this payment amount to your 2017 income tax return (see below). You should base your estimated payment on the net self-employment income plus half (the employer share) of the employment taxes on your self-employment income.
Here is information on how you enter your estimated payments in TurboTax:
https://ttlc.intuit.com/replies/3300049
