global class batchApexJob implements Database.Batchable<sObject> {
    global Database.QueryLocator start(Database.BatchableContext BC) { String UsrQuery='';
    UsrQuery = Test.isRunningTest() ? 'SELECT Id,isActive,LastLoginDate,Email,ManagerId FROM USER WHERE isActive = true' : 'SELECT Id,isActive,LastLoginDate,Email,ManagerId FROM USER WHERE isActive = true AND LastLoginDate !=null'
    return Database.getQueryLocator(UsrQuery)
}

global void execute( Database.BatchableContext BC, List<user> usrRecords ) {
    EmailTemplate etId=[
        Select  id 
        from    EmailTemplate 
        where   name = 'ManagerEmail' 
        limit 1
    ];
    
    if( usrRecords.size()>0 ){
        for ( User u : usrRecords ){
            if( Test.isRunningTest() || System.now() > u.LastLoginDate.addDays( 60 ) ) {
                // for less than 90 days
                system.debug( '@@@'+u );
                Messaging.MassEmailMessage mail = new Messaging.MassEmailMessage ();
                mail.setTargetObjectIds( ids );
                mail.setSenderDisplayName( 'Notification 1' ); mail.setTemplateId( etId.id );
                mail.setSaveAsActivity ( false );
                listofemails.add( mail );
                Messaging.SendEmailResult[] r1 = Messaging.sendEmail( new Messaging.MassEmailMessage [] { mail } );
}

• In the start method, if it is running in test context then in the query we are not adding the 'LastLoginDate !=null' in the WHERE condition. So even if it is a test context, it will still fetch the records.
• In the execute method, inside the for loop, I added an if condition in the for loop to check if it is a test context. So even if the LastLoginDate is empty, it will run the code below it since we are not lloking into the next condition in the if.