Now we have the e-way bill generation report available in Dynamics NAV 2016 CU33.
Below is the path
After selecting the option a new window will open, where you need to enter the filters off,
1. Date Filter
2. For which location you need the e-way bill.
3. Transaction Type: Customer or Vendor or Transfer.
4. Source Type will be filled automatically upon selection of transaction type.
5. Source No. : Here select the source no. i.e. customer no. or vendor no.
If you select Transaction Type as Transfer then you need to keep source no. blank, no need to enter any value.
After you click OK system shall generate an excel file.
Above Excel file will be generated which you can upload on the GSTN website to generate E-way bill.