The Letter of Consent is almost certainly better. One important reason is that you might be upgraded to a LTVP+ in the future (at your LTVP renewal), and that status would entitle you to lower medical fees at public hospitals and clinics (and lower Integrated Shield Plan premiums if I'm not mistaken, and if you choose to sign up for one). EPs don't enjoy these privileges.
As Valleyman pointed out, some employers are unfamiliar with LoCs, or at least they feign ignorance. The MoM
explains everything here clearly, and you can provide that link to your employer. The employer simply files a LoC application online, using the same online application (EP Online). Unlike an EP application there is no application fee, so the employer saves a little bit of money. There's also less paperwork to submit, fewer restrictions, and LoCs tend to be approved more quickly, allowing you to start work more quickly. You might mention these facts and perhaps express some mild incredulity that your employer would even think about taking a more difficult, more expensive path.
The only reason I can think of that an EP would be better for you is if you want to sponsor somebody (your parent, typically) for immigration into Singapore
now, your citizen or PR spouse (I presume) is not eligible to sponsor that relative, and you would meet the income requirement for sponsorship. However, if you only want to do that
later, your employer can file an EP application later -- you don't have to pursue that option now. One reason an EP might be better for the employer is that the employee is somewhat "stickier," that you'd be naturally more reluctant to leave or change jobs because you'd have to re-apply for a LTVP (or another EP). Also some employers are concerned that LTVP status is inherently dependent, so if your citizen or PR sponsor leaves Singapore then you must also. The employer would at least prefer the option to try to keep you in Singapore in that event, and an EP means they can try. But that's a weak argument, particularly for spouses of PRs and citizens, since you would need to agree to that plan anyway, and if you agree to that plan your employer could apply for an EP then, in the future.