You can do this either in iisnode.yml or in web.config. If you are deploying via git, you likely don't have those in your repo. You can get the default generated web.config by using Kudu Console and finding it under d:\home\site\wwwroot. By default, there is no iisnode.yml at all.
Using iisnode.yml
Just put the following line in the iisnode.yml:
nodeProcessCommandLine: node.exe --nouse-idle-notification --expose-gc --max-old-space-size=1024
Or if you use a full path to a version of Node, you'll need to quote it, e.g.
nodeProcessCommandLine: "D:\Program Files (x86)\nodejs\5.7.1\node.exe" --nouse-idle-notification --expose-gc --max-old-space-size=1024
Using web.config
Toward the end of the file, you'll see a commented out <iisnode> tag. Replace it by something like this:
<iisnode nodeProcessCommandLine="node.exe --nouse-idle-notification --expose-gc --max-old-space-size=1024"/>
Notes
iisnode.yml takes precedence over web.config
- I lowered your
max-old-space-size value as that was blowing up when I tried, but that's orthogonal.
Then with either file, you can commit them in your repo so it just works on deployment.