Prashant,
Check if the the Site Feature (not just site collection), for Nintex Workflow 2013 has been activated .
Site Settings >> manage Site Features.
Hello Prasanna,
Its already enabled. Still I am not able to see.
As of now I am generating URL manually and using it.
Create Site Workflow Link
site_url/_layouts/15/NintexWorkflow/WorkflowDesigner.aspx?Category=Site
Manage site workflow link
site_url/_layouts/15/NintexWorkflow/WorkflowGallery.aspx?Category=Site
Schedule site workflow link
site_url/_layouts/15/NintexWorkflow/WorkflowSchedules.aspx
You can try deactivate and then activate the Nintex Workflow features at the site level (don't forget to perform a backup before deactivating the features).
Hope this helps