Is there any way to use euca2ools natively on Windows or through Cygwin or is there any other tool compatible with eucalyptus which I could run under Windows ?
You can use the AWS CLI with Eucalyptus, e.g. for EC2:
aws --endpoint-url http://myeuca:8773/services/Eucalyptus ec2 describe-instances
the example assumes you have already configured credentials.