I spent a couple of days investigating the performance difference between JS/V8 and C, focusing first of all on the Hydrogen IR generated by the V8 engine. However, after making sure that no extraordinary optimizations are present there, I got back to the analysis of the assembly output and it struck me that the answer was a very simple one, boiling down to the couple of sentences in Jay Conrod's blog post on internals of V8:

According to the spec, all numbers in JavaScript are 64-bit floating point doubles. We frequently work with integers though, so V8 represents numbers with 31-bit signed integers whenever possible.

The example at hand allows fitting all computations in 32 bits and node.js takes full advantage of that! The C code utilizes the long type, which on OP's (as well as my) platform happens to be a 64-bit type. Thus, it is a 32-bit arithmetic vs 64-bit arithmetic issue, mostly due to the expensive division/remainder operation.

If long in the C code is replaced with int, then the binary produced by gcc beats node.js.

Also, if the loop is made to look for primes over a range that is outside the realm of 32-bit numbers the performance of the node.js version drops significantly.

Proof

The used source code is found further in the answer, below the results.

Counting primes less than 10 million with C and node.js

$ gcc count_primes.c -std=c99 -O3 -lm -o count_primes_long
$ sed 's/long/int/g; s/%li/%i/g' count_primes.c > count_primes_int.c
$ gcc count_primes_int.c -std=c99 -O3 -lm -o count_primes_int

# Count primes <10M using C code with (64-bit) long type
$ time ./count_primes_long 0 10000000
The range [0, 10000000) contains 664579 primes

real    0m4.394s
user    0m4.392s
sys 0m0.000s

# Count primes <10M using C code with (32-bit) int type
$ time ./count_primes_int 0 10000000
The range [0, 10000000) contains 664579 primes

real    0m1.386s
user    0m1.384s
sys 0m0.000s

# Count primes <10M using node.js/V8 which transparently does the
# job utilizing 32-bit types
$ time nodejs ./count_primes.js 0 10000000
The range [ 0 , 10000000 ) contains 664579 primes

real    0m1.828s
user    0m1.820s
sys 0m0.004s

Performance figures in the vicinity of the limit of signed 32-bit integers

Counting the primes in the range of length 100,000 starting at the number contained in the first column:

              | node.js | C (long) 
-----------------------------------
2,000,000,000 | 0.293s  | 0.639s    # fully within the 32-bit range
-----------------------------------
2,147,383,647 | 0.296s  | 0.655s    # fully within the 32-bit range
-----------------------------------
2,147,453,647 | 2.498s  | 0.646s    # 50% within the 32-bit range
-----------------------------------
2,147,483,647 | 4.717s  | 0.652s    # fully outside the 32-bit range
-----------------------------------
3,000,000,000 | 5.449s  | 0.755s    # fully outside the 32-bit range
-----------------------------------

count_primes.js

"use strict";

var isPrime = function(n){
    if (n < 2) {return false};
    if (n === 2) {return true};
    if (n === 3) {return true};
    if (n % 2 === 0) {return false};
    if (n % 3 === 0) {return false};
    var sqrtOfN = Math.sqrt(n);
    for (var i = 5; i <= sqrtOfN; i += 6){
        if (n % i === 0) {return false}
        if (n % (i + 2) === 0) {return false}
    }
    return true;
};

var countPrime = function(S, E){
    var count = 0;
    for (let i = S; i < E;i++){
        if ( isPrime(i) ) { ++count; }
    }
    return count;
};

if( process.argv.length != 4) {
    console.log('Usage: nodejs count_prime.js <range_start> <range_length>');
    process.exit();
}

var S = parseInt(process.argv[2]);
var N = parseInt(process.argv[3]);
var E = S+N;
var P = countPrime(S, E);
console.log('The range [', S, ',', E, ') contains', P, 'primes');

count_primes.c

#include <stdio.h>
#include <stdlib.h>
#include <math.h>

#define true 1
#define false 0

int isPrime (register long n){
    if (n < 2)      return false;
    if (n == 2)     return true;
    if (n == 3)     return true;
    if (n % 2 == 0) return false;
    if (n % 3 == 0) return false;
    double sqrtOfN = sqrt(n);
    for (long i = 5; i <= sqrtOfN; i += 6){
        if (n % i == 0) return false;
        if (n % (i + 2) == 0) return false;
    }
    return true;
};

int main(int argc, const char * argv[]) {
    if ( argc != 3 ) {
        fprintf(stderr, "Usage: count_primes <range_start> <range_length>\n");
        exit(1);
    }
    const long S = atol(argv[1]);
    const long N = atol(argv[2]);
    register long count = 0;
    for (register long i = S; i < S + N; i++){
        if ( isPrime(i) ) ++count;
    }
    printf("The range [%li, %li) contains %li primes\n", S, S+N, count);
}