No qualifying bean of type 'javax.persistence.EntityManager' available: expected single matching bean but found 2

You have defined two entitymanager. Now you have to tell spring which one should injected. For this you can use the @Qualifier Annotation:

@PersistenceContext(unitName = "company")
@Qualifier(<Name of the entitimanager you want to use>)
private EntityManager entityManager;

Found a solution by marking the class I was injecting with the EntityManager with @Component and then auto-wiring that class into the class that uses the GraphQLExecutor:

New class marked @Component

package p4;

import org.crygier.graphql.GraphQLExecutor;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.stereotype.Component;

import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;

@Component
public class CompanyGraphQLComponent {

  @PersistenceContext(unitName = "company")
  private EntityManager entityManager;

  public GraphQLExecutor graphQLExecutor() {
    return new GraphQLExecutor(entityManager);
  }
}

Class auto-wiring CompanyGraphQLComponent

package p4.rest.controllers;

import core_services.persistence.CompanyContextHolder;
import core_services.records.system.Company;
import graphql.ExecutionResult;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import p4.CompanyGraphQLComponent;
import p4.records.GraphQLQuery;

@RestController
public class GraphQLController {
  @Autowired
  private CompanyGraphQLComponent companyGraphQLComponent;

  @RequestMapping(value = "/graphql", consumes = MediaType.APPLICATION_JSON_VALUE)
  public ExecutionResult postJson(@RequestBody GraphQLQuery graphQLQuery) {
    return companyGraphQLComponent.graphQLExecutor().execute(graphQLQuery.getQuery(), graphQLQuery.getVariables());
  }
}