I can't file via NETFILE because I have self employment income while in Manitoba but as of December 31 I was living in Alberta. Is my only option to mail my return?

Yes, you would have to print and mail in your return. Unfortunately, TurboTax does not support Form T2203 Provincial and Territorial Taxes for 2017 - Multiple Jurisdictions. As well CRA will not allow you to NetFile with the form.

"You cannot use the NETFILE service if any of the following applies to you:

• You are filing an income tax and benefit return for the first time with the CRA and the CRA does not have your complete date of birth on record
• You went bankrupt in 2016 or 2017 (does not include proposal for bankruptcy)
• You are a non-resident of Canada
• You have income from a business with a permanent establishment outside your province or territory of residence (you have to complete Form T2203, Provincial and Territorial Taxes for 2016 - Multiple Jurisdictions)"

You should probably warn people about this before charging them for the home and business version of the software... I found that quite cruel