With help from @aldeed, there is now a swift3 branch of cordova-plugin-meteor-webapp that is compatible with Xcode 8. All plugin tests seem to pass on iOS 8, 9 and 10. A newly created app under Meteor 1.4.1.1 also seems to work correctly.
If you want to give it a try with your own app, you can add the latest version of the plugin using:
meteor add cordova:cordova-plugin-meteor-webapp@https://github.com/meteor/cordova-plugin-meteor-webapp.git#8bf95eed3f313299fc2de33658866278eea2cdc5
Xcode may ask you to convert to the latest Swift syntax when you open the project. You should select ‘Swift 3’ as the language version, and analysis should show that no code changes are necessary.